Re: [R] spatial analysis
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 06/12/11 03:06, Rolf Turner wrote: On 06/12/11 01:44, marianne.zeyrin...@ec.europa.eu wrote: Dear all, I am a PhD student in energy modelling. I am completely stuck with the following problem and would be very grateful for any kind of help. I have cells Don't we all? We're made of them. :-) What do you mean by ``I have''? I.e. be a bit more explicit about the nature of your data. and each cell is assigned a number. I would like to form clusters of cells where the sum of the cell numbers in each cluster must not exceed 250. One restriction is that only neighbouring cells Define neighbouring. can be formed into clusters. In the end I would like to have a list with all possible cell combinations. Do you mean all possible ways in which your ``collection of cells'' can be subdivided into such clusters? My guess is that the number of such ways could be extremely large. (Depending of course on how many cells there are in the collection.) Is it possible to do this with R If yes, I would very much appreciate all possible hints how to solve it. Install the fortunes package. Then type fortune(Yoda) But if you want useful help you'll have to make your question much clearer. Agreed - but as it is a spatial question, you should post it at r-sig-...@r-project.org, the list of the special interest group spatial analysis. I would also look into e.g. GRASS and SAGA, which might be faster with these kind of spatial calculations. In general, if I understand you correctly, you can start with each cell and then grow outwards until you hit your stop criteria (sum = 250), and then you should have your clusters: one solution per starting cell (assuming symmetric clusters - if the clusters can be a-symmetric, many many more). Cheers, Rainer cheers, Rolf Turner __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - -- Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany) Centre of Excellence for Invasion Biology Stellenbosch University South Africa Tel : +33 - (0)9 53 10 27 44 Cell: +33 - (0)6 85 62 59 98 Fax : +33 - (0)9 58 10 27 44 Fax (D):+49 - (0)3 21 21 25 22 44 email: rai...@krugs.de Skype: RMkrug -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAk7d0VYACgkQoYgNqgF2egqOsACfc6CKV1tY/0xbxR41AfwoBMtA bWsAnRivgAdiuF3MKErvl1l8I+twrOf+ =k9v+ -END PGP SIGNATURE- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to automate the detection of break points for use in cut
Dear R-users, I would like to know if there is a function (in base R or the extension packages) that would automatically detect the break points in a vector x for later use in the cut function. The idea is to determine the boundaries of the n intervals (n=1) delimiting clusters of data points which could be considered reasonably close, given a numerical vector x with unknown content and unknown multimodal distribution. For instance, given for the vector x defined by set.seed(1234); x - sort(c(rnorm(20,-1,0.1),rnorm( 10,5,0.1),rnorm(10,100,0.1))), this function would return a vector of 4 points: min(x), one value between 20 and 5, one value between 5 and 100, and max(x). Thank you in advance for your suggestions. Sebastien [[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 automate the detection of break points for use in cut
Obviously, cut would do the job if one knows the number of intervals in advance, which I assume I won't. I guess what I'm looking for is a function that figures out the number of intervals and their boundaries. Sebastien On Tue, Dec 6, 2011 at 3:29 AM, Sébastien Bihorel pomc...@free.fr wrote: Dear R-users, I would like to know if there is a function (in base R or the extension packages) that would automatically detect the break points in a vector x for later use in the cut function. The idea is to determine the boundaries of the n intervals (n=1) delimiting clusters of data points which could be considered reasonably close, given a numerical vector x with unknown content and unknown multimodal distribution. For instance, given for the vector x defined by set.seed(1234); x - sort(c(rnorm(20,-1,0.1),rnorm( 10,5,0.1),rnorm(10,100,0.1))), this function would return a vector of 4 points: min(x), one value between 20 and 5, one value between 5 and 100, and max(x). Thank you in advance for your suggestions. Sebastien [[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] factors with multiple levels
Hi R-experts, I'm running into some trouble with a multi-level factor. My apologies if this is a basic question, but I have been told there are different ways to do this and would like to see what you think. In the dataset I'm looking at, subjects named pictures multiple times (e.g., they named each picture 8 times), so Repetition is a multi-level factor. How would you enter it into a model? As a factor? Or a numeric predictor? I understand the pros and cons of both approaches, but there seems to be some debate about this. I am not interested in the individual contrasts between different levels of the Repetition factor, but only need the equivalent of an F value in a standard ANOVA for that factor. And what about dependencies between levels? Many thanks in advance, Agnieszka __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 view/edit large matrix/array in R?
Le lundi 05 décembre 2011 à 19:01 -0600, Michael a écrit : head, tail and fix commands don't really work well if I have large matrix/array for which I would like to be able to scroll up and dow, left and right ... Could anybody please help me? RKWard has a good data editor, and you can open several objects at the same time in tabs. But it will not probably work if your data set is really huge (here it works very well with a few thousand rows, though). If you need to see a selection of variables in parallel, ordering the variables so that they're next to each other is probably a good solution. Cheers __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Argument validation within functions
Hi,
I just started with writing functions in R and so some questions popped up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid for the
function. E.g argument a has to be a number in the range 0-1. How can that
easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives an error
message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is exectued as
part of if (or else). Is there a simpler way without having the if-brackets
around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with the next
line if no abort the function with a error message? How can such an error
message be created?
thank you and best regards,
/Johannes
--
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem in while loop
So I just ran your code verbatim with this one change and it finished
in less than 10 seconds. However, even without the change it doesn't
take more than 15 seconds: what exactly lead you to believe this was
an infinite loop?
Michael
On Tue, Dec 6, 2011 at 12:03 AM, R. Michael Weylandt
michael.weyla...@gmail.com michael.weyla...@gmail.com wrote:
Off the bat I'd suggest you vectorize loglikelihood as a simple one liner:
sum(log(b^2 + (x-a)^2))
That alone will speed up your function many times over: I'll look at the big
function in more detail tomorrow.
Michael
On Dec 5, 2011, at 10:37 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Thanks Michael
Lets figure out the problem by using the following function. I found the
same problem in this code too.
loglikehood - function(a, b = 0.1, x = c(-4.2, -2.85, -2.3, -1.02, 0.7,
0.98, 2.72, 3.5))
{
s - 0
for(i in 1:length(x)){
s - s + log(b^2 + (x[i] - a)^2)
}
s
}
loglikelihood(0.1)
simann - function(T0 = 1, N = 500, rho = 0.9, x0 = 0, eps = 0.1, f){
moving - 1
count - 0
Temp - T0
x - x0
while(moving 0){
moving - 0
for(i in 1:N){
y - x + runif(1,-eps,eps)
alpha - min(1,exp((f(x) -f(y))/Temp))
if(runif(1)alpha){
moving - moving +1
x - y
}
}
Temp - Temp*rho
count - count + 1
}
fmin - f(x)
return(c(x,fmin,count))
}
simann(f = loglikelihood)
I hope we can analyze every problems from this function
On Mon, Dec 5, 2011 at 10:27 PM, R. Michael Weylandt
michael.weyla...@gmail.com michael.weyla...@gmail.com wrote:
It's not necessarily equivalent to your loglikelihood function but since
that function wasn't provided I couldn't test it.
My broader point is this: you said the problem was that the loop ran
endlessly: I showed it does not run endlessly for at least one input so at
least part of the problem lies in loglikelihood, which, being unprovided, I
have trouble replicating.
My original guess still stands: it's either 1) a case of you getting stuck
at probaccept = 1 or 2) so slow it just feels endless. Either way, my
prescription is the same: print()
Michael
On Dec 5, 2011, at 9:30 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Yes, your function out- epiann(f = function(a,b) log(dnorm(a)*dnorm(b))),
N = 10) works well.
But why you are changing the loglikelihood function to f = function(a,b)
log(dnorm(a)*dnorm(b))? how it is equivalent to loglikelihood? is there any
mathematical relation? I also want to see the plot of aout and bout versus
loglikelihood, and see the cooling rate in different temperature. how is
this possible?
On Mon, Dec 5, 2011 at 6:07 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
If you run
out- epiann(f = function(a,b) log(dnorm(a)*dnorm(b))), N = 10)
It takes less than 0.5 seconds so there's no problem I can see:
perhaps you want to look elsewhere to get better speed (like Rcpp or
general vectorization), or maybe your loglikihood is not what's
desired, but there's no problem with the loop.
Michael
On Mon, Dec 5, 2011 at 5:29 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Yes, I checked the acceptprob, it is very high but in my view, the
while
loop is not stopping, so there is some thing wrong in the use of while
loop.
When I removed the while loop, it returned some thing but not the
result
what I want. When i run the while loop separately, it never stops.
On Mon, Dec 5, 2011 at 5:18 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Your code is not reproducible nor minimal, but why don't you put a
command print(acceptprob) in and see if you are getting reasonable
values. If these values are extremely low it shouldn't surprise you
that your loop takes a long time to run.
More generally, read up on the use of print() and browser() as
debugging
tools.
Michael
On Mon, Dec 5, 2011 at 3:47 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
I forgot to upload the R-code in last email, so heare is one
epiann - function(T0 = 1, N=1000, ainit=1, binit=1,rho = 0.99,
amean =
3,
bmean=1.6, avar =.1, bvar=.1, f){
moving - 1
count - 0
Temp - T0
aout - ainit
bout - binit
while(moving 0){
moving - 0
for (i in 1:N) {
aprop - rnorm (1,amean, avar)
bprop - rnorm (1,bmean, bvar)
if (aprop 0 bprop 0){
acceptprob - min(1,exp((f(aout, bout) -
f(aprop,bprop))/Temp))
u - runif(1)
if(uacceptprob){
moving - moving +1
aout - aprop
bout - bprop
}
else{aprob - aout
bprob - bout}
}
}
Temp - Temp*rho
count - count +1
}
Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radinger jradin...@gmx.at wrote:
Hi,
I just started with writing functions in R and so some questions popped up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid for the
function. E.g argument a has to be a number in the range 0-1. How can that
easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is exectued
as part of if (or else). Is there a simpler way without having the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with the
next line if no abort the function with a error message? How can such an
error message be created?
thank you and best regards,
/Johannes
--
__
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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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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] a question on autocorrelation acf
The code provided was the hard-to-find C part: there's also some R code involved that you can get in your console by typing acf without parentheses. I'm inclined to believe VR over any Excel implementation (and I don't know what pc is) but perhaps you can provide a (small) data-set using the dput() function and say what you are expecting to get from acf() instead. Michael On Mon, Dec 5, 2011 at 8:32 PM, Bazman76 h_a_patie...@hotmail.com wrote: Hi there, I have now cheked the results against pc give and the excel add-in poptools. Poptools and pc give get the same answer but R is quite different especially for the acf and pacf()? I looked at the book you recommended on p390 itshows the formulas and they look pretty standard. However looking at the code that you sent the acf function does not seem to be being calculated as shown in the book? At no point is the series mean calculated? unless the variable x is already demeaned in some way ie. there is some preprocessing that I need to see to fully understand? -- View this message in context: http://r.789695.n4.nabble.com/a-question-on-autocorrelation-acf-tp2076280p4163021.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] rugarch package: is this forecast correct?
The calculation is numerically stable on my machine: I'd mark it up as
computational/floating-point error and not worry about it.
Michael
On Mon, Dec 5, 2011 at 11:13 PM, Ivan Popivanov
ivan.popiva...@gmail.com wrote:
Let me start with the code:
library(quantmod)
library(rugarch)
getSymbols(SPY, from=1900-01-01)
rets=na.trim(diff(log(Cl(SPY
tt = tail(rets[/2004-10-29], 1000)
spec = ugarchspec(variance.model=list(garchOrder=c(1,1)),
mean.model=list(armaOrder=c(2,5)), distribution.model=sged)
for(ii in 1:10)
{
ttFit = ugarchfit( spec=spec, data=as.vector(tt), out.sample=0,
solver.control=list(trace=F) )
ttFore = ugarchforecast( ttFit, n.ahead=1, n.roll=0 )
print( as.array(ttFore)[,2,] )
}
Produces two different results: -0.001087313 and -0.001092084, each
repeated a few times.
What is the explanation for that? Since they are based on previous data, I
was expecting single step forecasts to produce the same result.
Thanks in advance!
Ivan
[[alternative HTML version deleted]]
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[R] Argument validation within functions
Adding on Michael comment:
If your trap all conditions that render your main code invalid at the
beginning of your code, the main code does not have to be within the else
part of a if else statement.
For instance:
myf - function(a,b,c){
if ( ! (is.numeric(a) (a=0 a=1) ) ){
stop('a is invalid')
}
if (all bad conditions for b){
stop('b is invalid')
}
if (all bad conditions for c){
stop('c is invalid')
}
return(a+b+c)
}
Sebastien
[[alternative HTML version deleted]]
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] help! what's wrong with setBreakpoint
On 11-12-05 10:32 PM, Michael wrote: Hi all, I am in the middle of debugging which is stopped using browser()... in myfile.R at around line #25. I was then stuck in a big loop which I want to escape and stop the program at the line after the big loop. In the debugging mode, I used Browse[2] setBreakpoint(myfile.R#38) What did it print? I then typed c and ENTER, thinking that it will continue to execute until when it comes across line #38 and then stop there... But it didn't work - it continued the execution until the end of the function, right at the line return(results)... What happened? How to solve this problem? One of the complications in R is that you can have multiple copies of a function in memory. You may (or may not, what did it print??) have set a breakpoint in one copy, then run another. Or you may have edited that function after originally sourcing it, and lost the source reference. An alternative to using setBreakpoint is just to edit a call to browser() into the function. It's less convenient, but more robust. Duncan Murdoch Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to automate the detection of break points for use in cut
On 11-12-06 3:34 AM, Sébastien Bihorel wrote: Obviously, cut would do the job if one knows the number of intervals in advance, which I assume I won't. I guess what I'm looking for is a function that figures out the number of intervals and their boundaries. That's not really a simple problem, but there are functions that do clustering and fit mixture models to data, which might be close enough. See the Cluster task view at http://cran.r-project.org/web/views/Cluster.html. Duncan Murdoch Sebastien On Tue, Dec 6, 2011 at 3:29 AM, Sébastien Bihorelpomc...@free.fr wrote: Dear R-users, I would like to know if there is a function (in base R or the extension packages) that would automatically detect the break points in a vector x for later use in the cut function. The idea is to determine the boundaries of the n intervals (n=1) delimiting clusters of data points which could be considered reasonably close, given a numerical vector x with unknown content and unknown multimodal distribution. For instance, given for the vector x defined by set.seed(1234); x- sort(c(rnorm(20,-1,0.1),rnorm( 10,5,0.1),rnorm(10,100,0.1))), this function would return a vector of 4 points: min(x), one value between 20 and 5, one value between 5 and 100, and max(x). Thank you in advance for your suggestions. Sebastien [[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] Argument validation within functions
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric? How can that be implemented in following
function:
f - function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: Johannes Radinger jradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can such an
error message be created?
thank you and best regards,
/Johannes
--
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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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and provide commented, minimal, self-contained, reproducible code.
[R] Paste() - Get all possible combinations from multiple vectors
Hello fellow R-users, Given are three vectors and the outcome would be all possible combinations in combination with the paste() function. For example: x - c(1:3) y - letters[1:3] z - LETTERS[1:3] My result would thus be 18 names based on all possible combinations between these vectors: 1 a A 1 a B, 1 a C, 1 b A, 1 b B, 1 b C, 1 c A, 1 c B, 1 c C, etc. To solve the issue above I would use: paste(rep(x, each=9), rep(y, each=6), z) This is a very straightforward example, but when I have vectors of different sizes, it will be much more difficult (for me) to create this. Is there an easier way to do this? Many thanks in advance, -- Stan [[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] Argument validation within functions
On 06.12.2011 13:46, Johannes Radinger wrote:
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric?
Yes, see:
?!
Uwe Ligges
How can that be implemented in following function:
f- function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandtmichael.weyla...@gmail.com
An: Johannes Radingerjradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radingerjradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a- as.numeric(a)
if(0= a a= 1)
to first check if a is a number...if not the function stops and gives an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can such an
error message be created?
thank you and best regards,
/Johannes
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Re: [R] Argument validation within functions
Use the ! (not) operator.
Not sure what you mean by as the stop() stops the total function:
try the following
f - function(a){
stopifnot(a 3)
return(a^2)
}
f(2)
f(4)
Michael
(PS -- It's usually asked to cc the list so that this all gets
threaded properly in folks' mailboxes)
On Tue, Dec 6, 2011 at 7:46 AM, Johannes Radinger jradin...@gmx.at wrote:
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric? How can that be implemented in following
function:
f - function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: Johannes Radinger jradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can such an
error message be created?
thank you and best regards,
/Johannes
--
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Re: [R] Paste() - Get all possible combinations from multiple vectors
outer(outer(x, y, paste), z, paste) Michael On Tue, Dec 6, 2011 at 7:53 AM, Gaj Stan (BIGCAT) stan@maastrichtuniversity.nl wrote: Hello fellow R-users, Given are three vectors and the outcome would be all possible combinations in combination with the paste() function. For example: x - c(1:3) y - letters[1:3] z - LETTERS[1:3] My result would thus be 18 names based on all possible combinations between these vectors: 1 a A 1 a B, 1 a C, 1 b A, 1 b B, 1 b C, 1 c A, 1 c B, 1 c C, etc. To solve the issue above I would use: paste(rep(x, each=9), rep(y, each=6), z) This is a very straightforward example, but when I have vectors of different sizes, it will be much more difficult (for me) to create this. Is there an easier way to do this? Many thanks in advance, -- Stan [[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] Can't load package 'lars'
On 06.12.2011 03:33, Luc Villandre wrote: Hi, I installed package 'lars' earlier tonight and did not get any sort of error message. ### ** building package indices ... ** testing if installed package can be loaded Loaded lars 0.9-8 * DONE (lars) ### However, when I try to load it, I get ### library(lars, lib.loc = ~/R/x86_64-redhat-linux-gnu-library/2.11) Are you sure it is installed at the location you specified? Uwe Ligges Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for ‘lars’ ### Session info: ### sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rpart_3.1-50 tools_2.14.0 ### I get the same error message when I try to load it on another machine: ### library(lars,lib.loc = ~/R/i686-pc-linux-gnu-library/2.12) Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for 'lars' ### Session info: ### sessionInfo() R version 2.13.1 (2011-07-08) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.1 ### Is there at least a way to circumvent the problem? Thank you for your help, Luc Villandre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Paste() - Get all possible combinations from multiple vectors
Hi. Maybe this will help you: expand.grid(x,y,z) apply(expand.grid(x,y,z),1, function (x) paste(x[1], x[2], x[3], sep=)) Andrija On Tue, Dec 6, 2011 at 1:53 PM, Gaj Stan (BIGCAT) stan@maastrichtuniversity.nl wrote: Hello fellow R-users, Given are three vectors and the outcome would be all possible combinations in combination with the paste() function. For example: x - c(1:3) y - letters[1:3] z - LETTERS[1:3] My result would thus be 18 names based on all possible combinations between these vectors: 1 a A 1 a B, 1 a C, 1 b A, 1 b B, 1 b C, 1 c A, 1 c B, 1 c C, etc. To solve the issue above I would use: paste(rep(x, each=9), rep(y, each=6), z) This is a very straightforward example, but when I have vectors of different sizes, it will be much more difficult (for me) to create this. Is there an easier way to do this? Many thanks in advance, -- Stan [[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] Regression model when dependent variable can only take positive values
Dear all, I would like to run a regression of the form lm(y ~ x1+x2) where the dependent variable y can only take positive values. Assume, for example, that y is the height of a person (measured in cm), x1 is the gender (measured as a binary indicator with 0=male and 1=female) and x2 is the age of the person (measured in years). When I run a simple lm(y ~ x1+x2), I obtain an intercept value that is negative. I interpret that in a way that a person who is male (x1=0) and just born (x2=0), has a negative height. This evidently does not make sense. I therefore assume that my estimates might be biased and that I need to use some other form of estimation that takes account of the fact that y0 for all observations. Could anybody please tell me which type of regression would be most recommendable for this type of analysis? Thanks very much in advance, Michael [[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] Summary coefficients give NA values because of singularities
On 05.12.2011 21:57, Gathurst wrote: Hello, I have a data set which I am using to find a model with the most significant parameters included and most importantly, the p-values. The full model is of the form: sad[,1]~b_1 sad[,2]+b_2 sad[,3]+b_3 sad[,4]+b_4 sad[,5]+b_5 sad[,6]+b_6 sad[,7]+b_7 sad[,8]+b_8 sad[,9]+b_9 sad[,10], where the 9 variables on the right hand side are all indicator variables. The thing I don't understand is the line ' sad[, 10] NA NA NA NA ' as a result of 'Coefficients: (1 not defined because of singularities)'. I think the output is taking sad[,10] as the intercept, based on previous attempts at figuring my issue out, which I find a bit wierd considering sad[,10] is either 0 or 1. How do I produce the correct output showing all p-values? You cannot: sad[,10] is either collinear to one or more of the other variables or is constant. Uwe Ligges My code and output is as follows: sad-matrix(1,ncol=11,nrow=486) sad[,c(1:10)]-d[,2][-357] sad[,1]-d[,29][-357] sad[,2][sad[,2]!=1]-0 sad[,3][sad[,3]!=2]-0 sad[,4][sad[,4]!=3]-0 sad[,5][sad[,5]!=4]-0 sad[,6][sad[,6]!=5]-0 sad[,7][sad[,7]!=6]-0 sad[,8][sad[,8]!=7]-0 sad[,9][sad[,9]!=8]-0 sad[,10][sad[,10]!=9]-0 sad[,2][sad[,2]==1]-1 sad[,3][sad[,3]==2]-1 sad[,4][sad[,4]==3]-1 sad[,5][sad[,5]==4]-1 sad[,6][sad[,6]==5]-1 sad[,7][sad[,7]==6]-1 sad[,8][sad[,8]==7]-1 sad[,9][sad[,9]==8]-1 sad[,10][sad[,10]==9]-1 sad summary(lm(sad[,1]~sad[,2]+sad[,3] +sad[,4]+sad[,5]+sad[,6] +sad[,7]+sad[,8]+sad[,9]+sad[,10])) Call: lm(formula = sad[, 1] ~ sad[, 2] + sad[, 3] + sad[, 4] + sad[, 5] + sad[, 6] + sad[, 7] + sad[, 8] + sad[, 9] + sad[, 10]) Residuals: Min 1Q Median 3Q Max -3.3191 -0.3893 0.0519 0.7436 1.0519 Coefficients: (1 not defined because of singularities) Estimate Std. Error t value Pr(|t|) (Intercept) 4.340910.14495 29.9472e-16 *** sad[, 2]-0.161420.18128 -0.890 0.3737 sad[, 3]-0.232210.20275 -1.145 0.2527 sad[, 4] 0.178320.19695 0.905 0.3657 sad[, 5] 0.064500.21447 0.301 0.7638 sad[, 6]-0.159090.18713 -0.850 0.3957 sad[, 7]-0.392860.18171 -2.162 0.0311 * sad[, 8]-0.084500.21146 -0.400 0.6896 sad[, 9]-0.021760.20170 -0.108 0.9141 sad[, 10] NA NA NA NA --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Residual standard error: 0.9615 on 477 degrees of freedom Multiple R-squared: 0.02984,Adjusted R-squared: 0.01357 F-statistic: 1.834 on 8 and 477 DF, p-value: 0.06869 Thanks in advance. -- View this message in context: http://r.789695.n4.nabble.com/Summary-coefficients-give-NA-values-because-of-singularities-tp4162113p4162113.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] Plot numeric and categorical variable
On 05.12.2011 23:22, Juliet Ndukum wrote: My data consists of numeric (yy) and categorical (xx) variables, as shown below. xx = c(rep(C, 5), rep(D,5)) xx [1] C C C C C D D D D D yy = rnorm(10, 0, 4) yy [1] 2.7219346 -3.7142481 6.8716534 -0.9352463 0.4901249 3.8113247 [7] -2.6602041 1.7714471 4.7298233 0.8848188 xx1 = as.integer(as.factor(xx)) plot(xx1, yy, ylim = c(-13.5, 4), col=blue) I have attached the plot above as plot1 I wish to generate a scatter plot of the data such that instead of 1 it prints C, and instead of 2, it prints D on the x- axis (see plot1 attached). How could I possibly go about this, let me know. Any help will be greatly appreciated. Thanks in advance for your help,JN Sounds like homework?! Anyway, see ?par and ?axis to answer your question directly or ?boxplot more implicitly... Best, Uwe Ligges __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Regression model when dependent variable can only take positive values
Dear Michael, Did you measure newborns? If not center age to a value that makes sense in relation with the range of age in your dataset. Then the intercept will be the height at the reference age. And most likeli non-negative. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Michael Haenlein Verzonden: dinsdag 6 december 2011 14:09 Aan: r-help@r-project.org Onderwerp: [R] Regression model when dependent variable can only take positive values Dear all, I would like to run a regression of the form lm(y ~ x1+x2) where the dependent variable y can only take positive values. Assume, for example, that y is the height of a person (measured in cm), x1 is the gender (measured as a binary indicator with 0=male and 1=female) and x2 is the age of the person (measured in years). When I run a simple lm(y ~ x1+x2), I obtain an intercept value that is negative. I interpret that in a way that a person who is male (x1=0) and just born (x2=0), has a negative height. This evidently does not make sense. I therefore assume that my estimates might be biased and that I need to use some other form of estimation that takes account of the fact that y0 for all observations. Could anybody please tell me which type of regression would be most recommendable for this type of analysis? Thanks very much in advance, Michael [[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] frequency table?
After that, you might consult the source code for distance() in ecodist. That function was specifically written to make it easy for people to add new dissimilarity/similarity metrics, and I think you'll find it helpful (even if you just extract the bit you need rather than expand the whole function). Sarah On Mon, Dec 5, 2011 at 9:40 PM, B77S bps0...@auburn.edu wrote: Set, This is the same post as your Similarity Matrix post. I'm not trying to be a smart ass here, but ... ?Can you fit a square peg in a round hole?... yes, but it doesn't mean it belongs there. I suggest you get a piece of paper and a pencil and figure out 1) what you are trying to do and why, and 2) how you would do that by hand. After you do that, you should be able to figure this out on your own or formulate a question to post that someone will be able to answer. Reading might help as well. set wrote Hello R-users, I've got a file with individuals as colums and the clusters where they occur in as rows. And I wanted a table which tells me how many times each individual occurs with another. I don't really know how such a table is called...it is not a frequency tableMy eventual goal is to make Venn-diagrams from the occurence of my individuals. So I've this: cluster ind1 ind2 ind3 etc. 1 0 1 2 2 3 0 1 3 1 1 1 And I want to go to this: ind1 ind2 ind3 ind1 0 4 2 ind2 4 0 4 ind3 2 4 1 is there a way to do this? Thank you for your help -- Sarah Goslee http://www.functionaldiversity.org __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with clusplot
Well, if I had to guess (and I do, since we have no idea what your data look like, and calling your data matrix is a very bad idea): you have more variables than units, so clusplot() can't use princomp() to create a reduced- dimension plot. You could roll your own using a different ordination method, or you could remove some variables from your data, or you could think about whether the data you have are appropriate for what you're trying to do with them. Sarah On Tue, Dec 6, 2011 at 12:58 AM, elisacarli21 elisacarl...@gmail.com wrote: Dear all I'm trying to run a cluster analysis with R Here are the commands: mydata - na.omit(matrix) # listwise deletion of missing mydata - scale(matrix) # standardize variables fit - kmeans(mydata, 8) # 8 cluster solution # get cluster means aggregate(mydata,by=list(fit$cluster),FUN=mean) # append cluster assignment mydata - data.frame(mydata, fit$cluster) library(cluster) clusplot(mydata, fit$cluster, color=TRUE, shade=TRUE, labels=2, lines=0) I get the following error Error in princomp.default(x, scores = TRUE, cor = ncol(x) != 2) : 'princomp' can only be used with more units than variables How can I fix it? Thanks -- 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] how to view/edit large matrix/array in R?
Michael comtech.usa at gmail.com writes: head, tail and fix commands don't really work well if I have large matrix/array for which I would like to be able to scroll up and dow, left and right ... Could anybody please help me? Thanks [[alternative HTML version deleted]] You might look into the RGtk2Extras package and find the dfedit. You could also embed that in some custom GUI to show variables, as you want. The package requires RGtk2, and hence the Gtk libraries to be installed. The data frame editor there can gracefully handle large data sets. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Plot numeric and categorical variable
Not to mention that I answered this exact question only yesterday. 2011/12/6 Uwe Ligges lig...@statistik.tu-dortmund.de: On 05.12.2011 23:22, Juliet Ndukum wrote: My data consists of numeric (yy) and categorical (xx) variables, as shown below. xx = c(rep(C, 5), rep(D,5)) xx [1] C C C C C D D D D D yy = rnorm(10, 0, 4) yy [1] 2.7219346 -3.7142481 6.8716534 -0.9352463 0.4901249 3.8113247 [7] -2.6602041 1.7714471 4.7298233 0.8848188 xx1 = as.integer(as.factor(xx)) plot(xx1, yy, ylim = c(-13.5, 4), col=blue) I have attached the plot above as plot1 I wish to generate a scatter plot of the data such that instead of 1 it prints C, and instead of 2, it prints D on the x- axis (see plot1 attached). How could I possibly go about this, let me know. Any help will be greatly appreciated. Thanks in advance for your help,JN Sounds like homework?! Anyway, see ?par and ?axis to answer your question directly or ?boxplot more implicitly... Best, Uwe Ligges -- 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] help! what's wrong with setBreakpoint
It printed: c:\R\myproject1\myfile.R#38: myfunc1 step 6,4,9 in environment: R_GlobalEnv What do you think? Thank you! On Tue, Dec 6, 2011 at 6:22 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 11-12-05 10:32 PM, Michael wrote: Hi all, I am in the middle of debugging which is stopped using browser()... in myfile.R at around line #25. I was then stuck in a big loop which I want to escape and stop the program at the line after the big loop. In the debugging mode, I used Browse[2] setBreakpoint(myfile.R#38) What did it print? I then typed c and ENTER, thinking that it will continue to execute until when it comes across line #38 and then stop there... But it didn't work - it continued the execution until the end of the function, right at the line return(results)... What happened? How to solve this problem? One of the complications in R is that you can have multiple copies of a function in memory. You may (or may not, what did it print??) have set a breakpoint in one copy, then run another. Or you may have edited that function after originally sourcing it, and lost the source reference. An alternative to using setBreakpoint is just to edit a call to browser() into the function. It's less convenient, but more robust. Duncan Murdoch Thanks a lot! [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help! what's wrong with setBreakpoint
On 06/12/2011 9:47 AM, Michael wrote: It printed: c:\R\myproject1\myfile.R#38: myfunc1 step 6,4,9 inenvironment: R_GlobalEnv What do you think? So that set a breakpoint in the copy of the function in the global environment. Are you sure you were executing the same function after you hit c? If you were working on code in a package, you may have been executing the function in the namespace of the package, not the one in the global environment. If that's not the case, then are you sure you ever got to that line? You can see where the breakpoint was set using body(myfunc1)[[c(6,4,9)]] (Watch the parens and brackets!) Duncan Murdoch Thank you! On Tue, Dec 6, 2011 at 6:22 AM, Duncan Murdochmurdoch.dun...@gmail.comwrote: On 11-12-05 10:32 PM, Michael wrote: Hi all, I am in the middle of debugging which is stopped using browser()... in myfile.R at around line #25. I was then stuck in a big loop which I want to escape and stop the program at the line after the big loop. In the debugging mode, I used Browse[2] setBreakpoint(myfile.R#38) What did it print? I then typed c and ENTER, thinking that it will continue to execute until when it comes across line #38 and then stop there... But it didn't work - it continued the execution until the end of the function, right at the line return(results)... What happened? How to solve this problem? One of the complications in R is that you can have multiple copies of a function in memory. You may (or may not, what did it print??) have set a breakpoint in one copy, then run another. Or you may have edited that function after originally sourcing it, and lost the source reference. An alternative to using setBreakpoint is just to edit a call to browser() into the function. It's less convenient, but more robust. Duncan Murdoch Thanks a lot! [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.htmlhttp://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] Read Windows BMP format images
Hello, Does anyone know of an R package that can read Windows BMP format images? Many thanks, Greg Jefferis. -- Gregory Jefferis, PhD Division of Neurobiology MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK. http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis http://www.neuroscience.cam.ac.uk/directory/profile.php?gsxej2 http://flybrain.stanford.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Writing out in loops
I would like to write some data to different files. I can create the
filename Day1.txt like this:
filen - paste(Day, l, .txt, sep=)
and then I'm using a For loop to write out one row of a matrix,
something like this:
For (j in 1:10)
{
cat(mat[1,j], ,, file=filen, append=TRUE)
}
cat(\n, file=filen, append=TRUE)
but is there a better way to do this?
Thank you,
Thomas
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[R] split date nad time
Dear R Users, given that: AggDateTime[960:962] [1] 2011-08-25 23:59:00 BST 2011-08-26 00:00:00 BST [3] 2011-08-26 00:01:00 BST unlist(strsplit(as.character(AggDateTime[960]), , fixed=TRUE)) [1] 2011-08-25 23:59:00 unlist(strsplit(as.character(AggDateTime[962]), , fixed=TRUE)) [1] 2011-08-26 00:01:00 Why no time here? unlist(strsplit(as.character(AggDateTime[961]), , fixed=TRUE)) [1] 2011-08-26 best, robert -- View this message in context: http://r.789695.n4.nabble.com/split-date-nad-time-tp4164191p4164191.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] MAC Problem with http in R while not problem on Win machine
Hello, thanks to (http://timelyportfolio.blogspot.com/) and also (http://systematicinvestor.wordpress.com) the following code was published and it is running smoothly on my Windows enviroment but it is failing to perform on my MAC. #get MAImp code from GIST #thanks to http://systematicinvestor.wordpress.com #for showing me how to do this con=url(https://raw.github.com/gist/1405187/92e7c24ff2459a0830c45b828f1dba41143e9436/MAImp.r;) source(con) the error code is the following Error in source(con) : cannot open the connection In addition: Warning message: In source(con) : unsupported URL scheme How can I amend the code that it will also work on my MAC ? many thanks martin -- __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] LaTeX output for summary.lm object - while displaying the information outside the table
Hi,Yes, you can use all values within the object For example, data(airquality) obj.lm - summary(lm(Temp~Ozone, airquality)) names(obj.lm) [1] call terms residuals coefficients aliased sigma [7] dfr.squared adj.r.squared fstatistic cov.unscaled na.action obj.lm$r.squared [1] 0.4877072 Then you have to manage the info to set the table as you want. I use latex() function from Hmisc package Best, Jose From: tal.gal...@gmail.com Date: Sun, 4 Dec 2011 16:57:51 +0200 To: r-help@r-project.org Subject: [R] LaTeX output for summary.lm object - while displaying the information outside the table This seemed to me to be basic, but I can't seem to find a solution online, so I wondered what I might be missing. I wish to include the output of an lm summary object inside an Sweave (.Rnw) document. I can either output the summary.lm as is, or use the xtable/Hmisc packages (through xtable or latex commands). Is there something like xtable that also gives the summary information which is available from outside the table? ( R2, F statistics etc...?) Thanks. Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- [[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] the estimated random effects for each level of grouping
Hi, I am a quite beginner of random effect modelling. Sorry for my ignorant question. My question is about the values of lme function. It returns coefficients which is a list with two components. The R-help file says that it returns the estimated random effects for each level of grouping. What is the estimator of this random effects in R? Since the random effects are random variables so this estimate should be something like mean or mode of the density of the random effect given data, f_i(b_i|y_i) -- View this message in context: http://r.789695.n4.nabble.com/the-estimated-random-effects-for-each-level-of-grouping-tp4164111p4164111.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] pls 2.3.0 released
Version 2.3.0 of the pls package has been released. The pls package implements Partial Least Squares Regression and Principal Component Regression. The major changes are: - New analysis method Canonical Powered PLS (CPPLS) implmemented. See ?cppls.fit. - coefplot() can now plot whiskers at +/-1 SE (since 2.2.0). See ?coefplot - The package now has a name space (since 2.2.0). -- Regards, Bjørn-Helge Mevik ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] HTML Forms to R
I have currently a R function that reads a csv file, does some computations, produces some plots and writes a csv file as output. I would like to use HTML forms to make a user interface for calling appropriate parts of the functions (reading csv file, doing computations, displaying plots and writing csv files). Are there are tutorials available that would help me get started?? Thank you. Ravi -- View this message in context: http://r.789695.n4.nabble.com/HTML-Forms-to-R-tp4164360p4164360.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] a question on autocorrelation acf
http://r.789695.n4.nabble.com/file/n4164630/R_example.xlsx R_example.xlsx
Hi there,
I attach an excel file which I use to produce the data.
It simulates a simple AR(1) process y_t=0.5y_{t-1}+z_t.
In column E I have cut and paste values so that we can compare like with
like.
When I run the acf() on these values, it shows 3 significant lags.
When I run the pacf() it shows one very strong correlation of 0.3 at lag 1,
and a smaller one at lag 2 of around 0.05.
Now according to the theory the pacf() results should give the correct
exponents for the lags.
This is a pure AR(1) process so the results should be 0.5 on lag 1 and
statistically insignificant else where?
I have tried if for several realisations of the white noise term and the
results are qualatively similar and is disagreement with the theory.
Kind Regards
Baz
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Re: [R] Writing out in loops
Is there some reason you can't create the entire file in R and then write it
out in a single step?
It looks like you're writing out
mat[1, 1:10]
so you could just use
write.table(mat[1, 1:10], filen)
Can you expand on what you're trying to do?
Sarah
On Tue, Dec 6, 2011 at 4:18 AM, Thomas chesney@gmail.com wrote:
I would like to write some data to different files. I can create the
filename Day1.txt like this:
filen - paste(Day, l, .txt, sep=)
and then I'm using a For loop to write out one row of a matrix, something
like this:
For (j in 1:10)
{
cat(mat[1,j], ,, file=filen, append=TRUE)
}
cat(\n, file=filen, append=TRUE)
but is there a better way to do this?
Thank you,
Thomas
--
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http://www.functionaldiversity.org
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Re: [R] How to automate the detection of break points for use in cut
I forgot to post my reply to Duncan's response on the list. On Tue, Dec 6, 2011 at 7:56 AM, Sébastien Bihorel pomc...@free.fr wrote: Thanks for the link Duncan, Given the number of methods and links listed in the Cluster task view, things are looking a bit more complex than I thought... I'll have to read more about clustering before I can start testing. Sebastien On Tue, Dec 6, 2011 at 7:28 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 11-12-06 3:34 AM, Sébastien Bihorel wrote: Obviously, cut would do the job if one knows the number of intervals in advance, which I assume I won't. I guess what I'm looking for is a function that figures out the number of intervals and their boundaries. That's not really a simple problem, but there are functions that do clustering and fit mixture models to data, which might be close enough. See the Cluster task view at http://cran.r-project.org/web/** views/Cluster.html http://cran.r-project.org/web/views/Cluster.html. Duncan Murdoch Sebastien On Tue, Dec 6, 2011 at 3:29 AM, Sébastien Bihorelpomc...@free.fr wrote: Dear R-users, I would like to know if there is a function (in base R or the extension packages) that would automatically detect the break points in a vector x for later use in the cut function. The idea is to determine the boundaries of the n intervals (n=1) delimiting clusters of data points which could be considered reasonably close, given a numerical vector x with unknown content and unknown multimodal distribution. For instance, given for the vector x defined by set.seed(1234); x- sort(c(rnorm(20,-1,0.1),rnorm( 10,5,0.1),rnorm(10,100,0.1))), this function would return a vector of 4 points: min(x), one value between 20 and 5, one value between 5 and 100, and max(x). Thank you in advance for your suggestions. Sebastien [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html 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] Argument validation within functions
Thank you, i didn't know that the !operator is
also working for is.numeric etc.
Anyway I want to test if an argument is set in the
function call and if not a code is executed... So
far I tried:
f -function(a,b){
if(!exists(b)) print(exists: b is not set)
if(is.null(b)) print(is.null : b is not set)
}
f(a=1,b=2)
f(a=1)
f(b=2)
I don't really know how to do it...e.g: for f(a=1) b is not set
so it also can't be NULL (thats why is.null is not working). I
just want to test if it is set with the function call not outside
the function or before etc.
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:57:44 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: r-help r-help@r-project.org, Johannes Radinger jradin...@gmx.at
Betreff: Re: [R] Argument validation within functions
Use the ! (not) operator.
Not sure what you mean by as the stop() stops the total function:
try the following
f - function(a){
stopifnot(a 3)
return(a^2)
}
f(2)
f(4)
Michael
(PS -- It's usually asked to cc the list so that this all gets
threaded properly in folks' mailboxes)
On Tue, Dec 6, 2011 at 7:46 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric? How can that be implemented in following
function:
f - function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: Johannes Radinger jradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions
popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid
for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives
an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having
the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can
such an
error message be created?
thank you and best regards,
/Johannes
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Re: [R] Argument validation within functions
G'day Johannes,
On Tue, 06 Dec 2011 16:15:21 +0100
Johannes Radinger jradin...@gmx.at wrote:
Thank you, i didn't know that the !operator is
also working for is.numeric etc.
Anyway I want to test if an argument is set in the
function call and if not a code is executed... So
far I tried:
f -function(a,b){
if(!exists(b)) print(exists: b is not set)
if(is.null(b)) print(is.null : b is not set)
}
f(a=1,b=2)
f(a=1)
f(b=2)
I don't really know how to do it...e.g: for f(a=1) b is not set
so it also can't be NULL (thats why is.null is not working). I
just want to test if it is set with the function call not outside
the function or before etc.
?missing
Cheers,
Berwin
== Full address
A/Prof Berwin A Turlach Tel.: +61 (8) 6488 3338 (secr)
School of Maths and Stats (M019)+61 (8) 6488 3383 (self)
The University of Western Australia FAX : +61 (8) 6488 1028
35 Stirling Highway
Crawley WA 6009e-mail: berwin.turl...@gmail.com
Australiahttp://www.maths.uwa.edu.au/~berwin
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Re: [R] Problem in while loop
Yes Michael, it works well and I got the result what I want but it totally
depends on how reliable result do I want. When I take very high rho (near
about 1) and very low psi, it takes very long time may be it gives us more
accurate result. But for lower rho and higher psi, it gives immediately,
and very poor result. Now as I asked before, how I can get the plot of a
versus s which determines the cooling curve with the global minimum of s
at a specific value of a.
On Tue, Dec 6, 2011 at 6:52 AM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
So I just ran your code verbatim with this one change and it finished
in less than 10 seconds. However, even without the change it doesn't
take more than 15 seconds: what exactly lead you to believe this was
an infinite loop?
Michael
On Tue, Dec 6, 2011 at 12:03 AM, R. Michael Weylandt
michael.weyla...@gmail.com michael.weyla...@gmail.com wrote:
Off the bat I'd suggest you vectorize loglikelihood as a simple one
liner:
sum(log(b^2 + (x-a)^2))
That alone will speed up your function many times over: I'll look at the
big
function in more detail tomorrow.
Michael
On Dec 5, 2011, at 10:37 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Thanks Michael
Lets figure out the problem by using the following function. I found the
same problem in this code too.
loglikehood - function(a, b = 0.1, x = c(-4.2, -2.85, -2.3, -1.02, 0.7,
0.98, 2.72, 3.5))
{
s - 0
for(i in 1:length(x)){
s - s + log(b^2 + (x[i] - a)^2)
}
s
}
loglikelihood(0.1)
simann - function(T0 = 1, N = 500, rho = 0.9, x0 = 0, eps = 0.1, f){
moving - 1
count - 0
Temp - T0
x - x0
while(moving 0){
moving - 0
for(i in 1:N){
y - x + runif(1,-eps,eps)
alpha - min(1,exp((f(x) -f(y))/Temp))
if(runif(1)alpha){
moving - moving +1
x - y
}
}
Temp - Temp*rho
count - count + 1
}
fmin - f(x)
return(c(x,fmin,count))
}
simann(f = loglikelihood)
I hope we can analyze every problems from this function
On Mon, Dec 5, 2011 at 10:27 PM, R. Michael Weylandt
michael.weyla...@gmail.com michael.weyla...@gmail.com wrote:
It's not necessarily equivalent to your loglikelihood function but
since
that function wasn't provided I couldn't test it.
My broader point is this: you said the problem was that the loop ran
endlessly: I showed it does not run endlessly for at least one input so
at
least part of the problem lies in loglikelihood, which, being
unprovided, I
have trouble replicating.
My original guess still stands: it's either 1) a case of you getting
stuck
at probaccept = 1 or 2) so slow it just feels endless. Either way, my
prescription is the same: print()
Michael
On Dec 5, 2011, at 9:30 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Yes, your function out- epiann(f = function(a,b)
log(dnorm(a)*dnorm(b))),
N = 10) works well.
But why you are changing the loglikelihood function to f = function(a,b)
log(dnorm(a)*dnorm(b))? how it is equivalent to loglikelihood? is there
any
mathematical relation? I also want to see the plot of aout and bout
versus
loglikelihood, and see the cooling rate in different temperature. how is
this possible?
On Mon, Dec 5, 2011 at 6:07 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
If you run
out- epiann(f = function(a,b) log(dnorm(a)*dnorm(b))), N = 10)
It takes less than 0.5 seconds so there's no problem I can see:
perhaps you want to look elsewhere to get better speed (like Rcpp or
general vectorization), or maybe your loglikihood is not what's
desired, but there's no problem with the loop.
Michael
On Mon, Dec 5, 2011 at 5:29 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
Yes, I checked the acceptprob, it is very high but in my view, the
while
loop is not stopping, so there is some thing wrong in the use of
while
loop.
When I removed the while loop, it returned some thing but not the
result
what I want. When i run the while loop separately, it never stops.
On Mon, Dec 5, 2011 at 5:18 PM, R. Michael Weylandt
michael.weyla...@gmail.com wrote:
Your code is not reproducible nor minimal, but why don't you put a
command print(acceptprob) in and see if you are getting reasonable
values. If these values are extremely low it shouldn't surprise you
that your loop takes a long time to run.
More generally, read up on the use of print() and browser() as
debugging
tools.
Michael
On Mon, Dec 5, 2011 at 3:47 PM, Gyanendra Pokharel
gyanendra.pokha...@gmail.com wrote:
I forgot to upload the R-code in last email, so heare is one
epiann - function(T0 = 1, N=1000, ainit=1, binit=1,rho = 0.99,
amean =
3,
bmean=1.6, avar =.1, bvar=.1, f){
moving - 1
count - 0
Temp - T0
Re: [R] Argument validation within functions
you may be looking for ?missing
f - function(a,b) {
if (missing(b)) print(b is missing)
}
f(a=1, b=2)
f(a=1)
f(b=2)
Regards,
Enrico
Am 06.12.2011 16:15, schrieb Johannes Radinger:
Thank you, i didn't know that the !operator is
also working for is.numeric etc.
Anyway I want to test if an argument is set in the
function call and if not a code is executed... So
far I tried:
f-function(a,b){
if(!exists(b)) print(exists: b is not set)
if(is.null(b)) print(is.null : b is not set)
}
f(a=1,b=2)
f(a=1)
f(b=2)
I don't really know how to do it...e.g: for f(a=1) b is not set
so it also can't be NULL (thats why is.null is not working). I
just want to test if it is set with the function call not outside
the function or before etc.
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:57:44 -0500
Von: R. Michael Weylandtmichael.weyla...@gmail.com
An: r-helpr-help@r-project.org, Johannes Radingerjradin...@gmx.at
Betreff: Re: [R] Argument validation within functions
Use the ! (not) operator.
Not sure what you mean by as the stop() stops the total function:
try the following
f- function(a){
stopifnot(a 3)
return(a^2)
}
f(2)
f(4)
Michael
(PS -- It's usually asked to cc the list so that this all gets
threaded properly in folks' mailboxes)
On Tue, Dec 6, 2011 at 7:46 AM, Johannes Radingerjradin...@gmx.at
wrote:
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric? How can that be implemented in following
function:
f- function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandtmichael.weyla...@gmail.com
An: Johannes Radingerjradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radingerjradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions
popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid
for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a- as.numeric(a)
if(0= a a= 1)
to first check if a is a number...if not the function stops and gives
an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having
the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can
such an
error message be created?
thank you and best regards,
/Johannes
--
__
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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Lucerne, Switzerland
http://nmof.net/
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[R] About summary in linear models
Hello!!, for linear models fit I use Gretl, but now I'm starting to use R, I would like to know if is there some function to obtain a extended summary like in Gretl. I will write a example in Gretl Modelo 1: MCO, usando las observaciones 1968-1982 (T = 15) Variable dependiente: Invest Coeficient St error t-ratio p-value const 377,631 35,0955 10,7601 0,1 *** GNP 0,63612 0,055015 11,5627 0,1 *** CPI -9,70228 0,913737 -10,6182 0,1 *** Interest -0,941363 2,21077 -0,4258 0,67927 time 8,49182 3,18142 2,6692 0,02353 ** Average of Dep Var. 276,0067 St Error Dep. Var 117,5827 Squared Sum of remainders 818,6362 Regression standar error 9,047852 R^2 0,995771 R^2 adj 0,994079 F(4, 10) 588,6040 p-value (de F) 8,09e-12 Log-likelihood -51,28100 Akaike 112,5620 Schwarz 116,1023 Hannan-Quinn 112,5243 rho -0,440663 Durbin-Watson 2,757428 Like you can see Gretl shows more statisticas. The same model in R: Call: lm(formula = Invest ~ CPI + GNP + Interest + Year, data = Tabla6_3) Residuals: Min 1Q Median 3Q Max -16.397 -3.864 1.391 4.219 15.779 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1.633e+04 6.250e+03 -2.612 0.0260 * CPI -9.702e+00 9.137e-01 -10.618 9.15e-07 *** GNP 6.361e-01 5.502e-02 11.563 4.14e-07 *** Interest-9.414e-01 2.211e+00 -0.426 0.6793 Year 8.492e+00 3.181e+00 2.669 0.0235 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Thanks so much, Otto [[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] Argument validation within functions
On Tue, Dec 6, 2011 at 7:15 AM, Johannes Radinger jradin...@gmx.at wrote:
Thank you, i didn't know that the !operator is
also working for is.numeric etc.
Read (more carefully?) R docs, please. ! is a unary function that
takes a logical argument(and will coerce to logical nonlogical
arguments if it can); is.numeric() returns a logical, so of course it
should work. Ergo your failure to understand indicates a fundamental
hole in your understanding of how R works.
-- Bert
Anyway I want to test if an argument is set in the
function call and if not a code is executed... So
far I tried:
f -function(a,b){
if(!exists(b)) print(exists: b is not set)
if(is.null(b)) print(is.null : b is not set)
}
f(a=1,b=2)
f(a=1)
f(b=2)
I don't really know how to do it...e.g: for f(a=1) b is not set
so it also can't be NULL (thats why is.null is not working). I
just want to test if it is set with the function call not outside
the function or before etc.
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:57:44 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: r-help r-help@r-project.org, Johannes Radinger jradin...@gmx.at
Betreff: Re: [R] Argument validation within functions
Use the ! (not) operator.
Not sure what you mean by as the stop() stops the total function:
try the following
f - function(a){
stopifnot(a 3)
return(a^2)
}
f(2)
f(4)
Michael
(PS -- It's usually asked to cc the list so that this all gets
threaded properly in folks' mailboxes)
On Tue, Dec 6, 2011 at 7:46 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
thank you... I think I will go for the if-stop approach
as the stop() stops the total function... So there is just
one little other question: What is the opposite of is.numeric?
Is ther isnot.numeric? How can that be implemented in following
function:
f - function(a){
if(is.numeric(a)) stop(a is not numeric)
if(0 a a 1) stop(a must be a value between 0 and 1)
a
}
/Johannes
Original-Nachricht
Datum: Tue, 6 Dec 2011 07:04:59 -0500
Von: R. Michael Weylandt michael.weyla...@gmail.com
An: Johannes Radinger jradin...@gmx.at
CC: r-help@r-project.org
Betreff: Re: [R] Argument validation within functions
The quick and dirty way to do so is to use: stopifnot() in conjunction
(if necessary with all() and any()). You can replace that first
condition with a simple is.numeric() as well. A more helpful way (if
this is production code) is to use if statement with the stop()
function directly which lets you provide specific error messages.
Michael
On Tue, Dec 6, 2011 at 6:41 AM, Johannes Radinger jradin...@gmx.at
wrote:
Hi,
I just started with writing functions in R and so some questions
popped
up.
I provide some values as argument to my function such as:
function(a,b,c){}
Now i want that the function first checks if the arguments are valid
for
the function. E.g argument a has to be a number in the range 0-1. How
can that easily done?
So far I have:
a - as.numeric(a)
if(0 = a a = 1)
to first check if a is a number...if not the function stops and gives
an
error message. If it is a number it just continues...
But how to check the range?
Above there is the if-approach but then the rest of the function is
exectued as part of if (or else). Is there a simpler way without having
the
if-brackets around the remaining code?
Just a check if the value is between 0 and 1 and if yes continue with
the next line if no abort the function with a error message? How can
such an
error message be created?
thank you and best regards,
/Johannes
--
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
NEU: FreePhone - 0ct/min Handyspartarif mit Geld-zurück-Garantie!
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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.
--
Bert Gunter
Genentech Nonclinical Biostatistics
Internal Contact Info:
Phone: 467-7374
Website:
http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm
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Re: [R] help! what's wrong with setBreakpoint
I am not sure... How do I make sure about that? esp Are you sure you were executing the same function after you hit c?? Thanks again! On Tue, Dec 6, 2011 at 8:57 AM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 06/12/2011 9:47 AM, Michael wrote: It printed: c:\R\myproject1\myfile.R#38: myfunc1 step 6,4,9 inenvironment: R_GlobalEnv What do you think? So that set a breakpoint in the copy of the function in the global environment. Are you sure you were executing the same function after you hit c? If you were working on code in a package, you may have been executing the function in the namespace of the package, not the one in the global environment. If that's not the case, then are you sure you ever got to that line? You can see where the breakpoint was set using body(myfunc1)[[c(6,4,9)]] (Watch the parens and brackets!) Duncan Murdoch Thank you! On Tue, Dec 6, 2011 at 6:22 AM, Duncan Murdochmurdoch.duncan@gmail.**commurdoch.dun...@gmail.com wrote: On 11-12-05 10:32 PM, Michael wrote: Hi all, I am in the middle of debugging which is stopped using browser()... in myfile.R at around line #25. I was then stuck in a big loop which I want to escape and stop the program at the line after the big loop. In the debugging mode, I used Browse[2] setBreakpoint(myfile.R#38) What did it print? I then typed c and ENTER, thinking that it will continue to execute until when it comes across line #38 and then stop there... But it didn't work - it continued the execution until the end of the function, right at the line return(results)... What happened? How to solve this problem? One of the complications in R is that you can have multiple copies of a function in memory. You may (or may not, what did it print??) have set a breakpoint in one copy, then run another. Or you may have edited that function after originally sourcing it, and lost the source reference. An alternative to using setBreakpoint is just to edit a call to browser() into the function. It's less convenient, but more robust. Duncan Murdoch Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**http://www.r-project.org/** posting-guide.htmlhttp://www.**r-project.org/posting-guide.**htmlhttp://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] split date nad time
On Dec 6, 2011, at 5:38 AM, threshold wrote: Dear R Users, given that: AggDateTime[960:962] [1] 2011-08-25 23:59:00 BST 2011-08-26 00:00:00 BST [3] 2011-08-26 00:01:00 BST unlist(strsplit(as.character(AggDateTime[960]), , fixed=TRUE)) [1] 2011-08-25 23:59:00 unlist(strsplit(as.character(AggDateTime[962]), , fixed=TRUE)) [1] 2011-08-26 00:01:00 Why no time here? unlist(strsplit(as.character(AggDateTime[961]), , fixed=TRUE)) [1] 2011-08-26 The real question should be: why you didn't post the results of : dput(AggDateTime[960:962]) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] mfp package - can I exclude some powers?
Hi, The mfp package suggests fractional polynomial transformations for non-linear predictors. For continuous variables that take negative values the suggested transformations tend to look ugly, e.g. if x1 is the original variable it is transformed to something like: (x1+5.67)^1 * log(x1+5.67), where 5.67 is the shift to make it positive. Can I somehow modify the mfp function to exclude some powers among those tried (e.g. those involving log and 0.5). I am willing to sacrifice some precision for a more interpretable transformation. Or is there another package to do something similar? Any suggestions very much appreciated! Eleni Medical Statistician Epidemiology Public Health University College London, UK __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] axis thickness in plot()
Hello, I am trying to increase the thickness of the axis in plot() without reverting to the use of paint programs i see posts on that topic for the xyplot function but want to see if i can do it with plot() because i've already setup my graph script using that i thought i could use axis() function and specify lwd=thickness or lwd.axis= but that does not work like it does for lwd.ticks If anyone has an idea, sincerely heres the script windows(width=7,height=7) plot(data$Winter,data$NbFirstBroods,ylab=number of breeding pairs,xlab=winter harshness,cex=1.5,cex.lab=1.5,cex.axis=1.5,font.axis=2,axes=FALSE) points(data$Winter,data$NbFirstBroods,cex=1.5,col=black,pch=19) abline(lm(data$NbFirstBroods~data$Winter),col=red,lwd=4) i tried axis(1, lwd.axis = 3,lwd.ticks=3) for example also when adding the y axis axis(2...) x and y axes are disconnected Thank you for your kind help in advance, Alexandre -- View this message in context: http://r.789695.n4.nabble.com/axis-thickness-in-plot-tp4165430p4165430.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] split date nad time
ok, dput(AggDateTime[960:962]) structure(c(1314313140L, 1314313200L, 1314313260L), class = c(POSIXct, POSIXt), tzone = ) -- View this message in context: http://r.789695.n4.nabble.com/split-date-nad-time-tp4164191p4165378.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 wrapping findInterval into a function
Dear R Community,
I hope you might be able to assist with a small problem creating a function.
I am working with water-quality data sets that contain the concentration of
many different elements in water samples. I need to assign quality-control
flags to values that fall into various concentration ranges. Rather than a
web of nested if statements, I am employing the findInterval function to
identify values that need to be flagged and to assign the appropriate flag.
The data consist of a sample identifier, the analysis, and corresponding
value. The findInterval function works well; however, I would like to
incorporate it into a function so that I can run multiple findInterval
functions for many different water-quality analyses (and I have to do this
for many dataset) but it seems to fall apart when incorporated into a
function.
Run straighforward, the findInterval function works as desired, e.g. below,
creating the new CalciumFlag column with the appropriate flag for, in this
case, levels of calcium in the water:
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium, (flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1, 100,
Inf))]),))
However, it does not worked when wrapped in a function (no error messages
are thrown, it simply does not seem to do anything):
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium, (flags
-
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1, 100,
Inf))]),))
}
Calling the function WQfunc() does not produce an error but also does not
produce the expected CalciumFlag, it seems to not do anything.
Ultimately, what I need to get to is something like below where multiple
findInterval functions for different analyses are included in a single
function, then I can concatenate the results into a single column containing
all flags for all analyses, e.g.:
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium, (flags
-
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1, 100,
Inf))]),))
WQdata$SodiumFlag - with(WQdata, ifelse(analysis == Sodium, (flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.050, 0.125, 125,
Inf))]),))
WQdata$MagnesiumFlag - with(WQdata, ifelse(analysis == Magnesium,
(flags
- c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.065, 0.15, 75,
Inf))]),))
.etc for additional water-quality analyses...
}
As an aside, I started working with the findInterval tool from an example
that I found online but am not clear as to how the multi-component
configuration incorporating brackets actually works, can anyone suggest a
good resource that explains this?
I thank you very much for any assistance you may be able to provide.
Regards,
Steve
--
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Sent from the R help mailing list archive at Nabble.com.
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Re: [R] About summary in linear models
Your email has become a bit distorted during transmission. If you have used the summary command you should be getting some more summary statistics. The lm function in R returns an object of class lm which is a list containing at least the components listed in the help files for lm. The objects in the list are used to produce the summary statistics. If you are doing more elaborate work this approach (like the use of internal functions in gretl) is very convenient. Best Regards John On 6 December 2011 15:28, Otto F. Wagner ofwag...@gmail.com wrote: Hello!!, for linear models fit I use Gretl, but now I'm starting to use R, I would like to know if is there some function to obtain a extended summary like in Gretl. I will write a example in Gretl Modelo 1: MCO, usando las observaciones 1968-1982 (T = 15) Variable dependiente: Invest Coeficient St error t-ratio p-value const 377,631 35,0955 10,7601 0,1 *** GNP 0,63612 0,055015 11,5627 0,1 *** CPI -9,70228 0,913737 -10,6182 0,1 *** Interest -0,941363 2,21077 -0,4258 0,67927 time 8,49182 3,18142 2,6692 0,02353 ** Average of Dep Var. 276,0067 St Error Dep. Var 117,5827 Squared Sum of remainders 818,6362 Regression standar error 9,047852 R^2 0,995771 R^2 adj 0,994079 F(4, 10) 588,6040 p-value (de F) 8,09e-12 Log-likelihood -51,28100 Akaike 112,5620 Schwarz 116,1023 Hannan-Quinn 112,5243 rho -0,440663 Durbin-Watson 2,757428 Like you can see Gretl shows more statisticas. The same model in R: Call: lm(formula = Invest ~ CPI + GNP + Interest + Year, data = Tabla6_3) Residuals: Min 1Q Median 3Q Max -16.397 -3.864 1.391 4.219 15.779 Coefficients: Estimate Std. Error t value Pr(|t|) (Intercept) -1.633e+04 6.250e+03 -2.612 0.0260 * CPI -9.702e+00 9.137e-01 -10.618 9.15e-07 *** GNP 6.361e-01 5.502e-02 11.563 4.14e-07 *** Interest -9.414e-01 2.211e+00 -0.426 0.6793 Year 8.492e+00 3.181e+00 2.669 0.0235 * --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Thanks so much, Otto [[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. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] help! browser() does not get stopped...
It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Please help me! Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help! browser() does not get stopped...
On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! 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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Can't load package 'lars'
On 06.12.2011 18:27, Luc Villandre wrote: Hello, I do think so. ### [villandre@stat04 lars]$ pwd /home/villandre/R/x86_64-redhat-linux-gnu-library/2.11/lars [villandre@stat04 lars]$ ls data DESCRIPTION help html INDEX libs Meta NAMESPACE R ### I re-installed it and I still get the same error message. install.packages(lars, lib = ~/R/x86_64-redhat-linux-gnu-library/2.11) trying URL 'http://software.rc.fas.harvard.edu/mirrors/R/src/contrib/lars_0.9-8.tar.gz' Content type 'application/x-gzip' length 172011 bytes (167 Kb) opened URL == downloaded 167 Kb * installing *source* package ‘lars’ ... ** libs gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c delcol.f -o delcol.o gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o lars.so delcol.o -lgfortran -lm -L/usr/lib64/R/lib -lR installing to /mnt/prism/s20/villandre/R/x86_64-redhat-linux-gnu-library/2.11/lars/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices converting help for package ‘lars’ finding HTML links ... done cv.lars html diabeteshtml lars-internal html larshtml plot.lars html predict.larshtml summary.larshtml ** building package indices ... ** testing if installed package can be loaded Loaded lars 0.9-8 * DONE (lars) The downloaded packages are in ‘/tmp/RtmphxCj4j/downloaded_packages’ library(lars, lib.loc = ~/R/x86_64-redhat-linux-gnu-library/2.11) Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds I haven't looked closely enough before: The culprit is in lars which has: cat(Loaded lars, utils::installed.packages()[lars, Version], and hence only looks at the default search path to report its version while you supplied a different one. Thus, it is a bug in the package you should report to its maintainer. I the meantime as a workaround (and maybe more convenient anyway): set the location of your library using .libPaths() before loading the package. Uwe Ligges Error: package/namespace load failed for ‘lars’ It is the first time I get such an error message when trying to load a package. It would seem that the problem is with ### cat(Loaded lars, utils::installed.packages()[lars, Version] ### Is there a way to circumvent this problem (e.g. attribute an arbitrary value to utils::installed.packages()[lars, Version])? Thanks for your help, Luc From: Uwe Ligges [lig...@statistik.tu-dortmund.de] Sent: Tuesday, December 06, 2011 8:01 AM To: Luc Villandre Cc: r-help Subject: Re: [R] Can't load package 'lars' On 06.12.2011 03:33, Luc Villandre wrote: Hi, I installed package 'lars' earlier tonight and did not get any sort of error message. ### ** building package indices ... ** testing if installed package can be loaded Loaded lars 0.9-8 * DONE (lars) ### However, when I try to load it, I get ### library(lars, lib.loc = ~/R/x86_64-redhat-linux-gnu-library/2.11) Are you sure it is installed at the location you specified? Uwe Ligges Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for ‘lars’ ### Session info: ### sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rpart_3.1-50 tools_2.14.0 ### I get the same error message when I try to load it on another machine: ### library(lars,lib.loc = ~/R/i686-pc-linux-gnu-library/2.12) Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for 'lars' ### Session info: ### sessionInfo() R version 2.13.1 (2011-07-08) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages:
Re: [R] help! what's wrong with setBreakpoint
On 06/12/2011 11:11 AM, Michael wrote: I am not sure... How do I make sure about that? esp Are you sure you were executing the same function after you hit c?? From a later one of your messages (adding a call to browser() didn't do anything), I think you weren't. Now you know how to check. Debugging code in packages can be tricky. There are several strategies that I've used in different circumstances: 1. source() the original source files from the command line. Then you're not in a namespace, so you don't have that to confuse you. (But if you don't source everything, you may find the source'd functions can't see the ones you skipped.) 2. Set the environment variable R_KEEP_PKG_SOURCE to yes, then install the package; do all my debugging via things like setBreakpoint(srcfile.R#30, env=somefunction) where somefunction is in the package being debugged. You can't make permanent changes to the functions this way, but you can add debugging code in the setBreakpoint call. 3. Edit the source and re-install the package. This is a bit of a pain, but it's the best way to reproduce the real execution environment. Duncan Murdoch Thanks again! On Tue, Dec 6, 2011 at 8:57 AM, Duncan Murdochmurdoch.dun...@gmail.comwrote: On 06/12/2011 9:47 AM, Michael wrote: It printed: c:\R\myproject1\myfile.R#38: myfunc1 step 6,4,9 inenvironment: R_GlobalEnv What do you think? So that set a breakpoint in the copy of the function in the global environment. Are you sure you were executing the same function after you hit c? If you were working on code in a package, you may have been executing the function in the namespace of the package, not the one in the global environment. If that's not the case, then are you sure you ever got to that line? You can see where the breakpoint was set using body(myfunc1)[[c(6,4,9)]] (Watch the parens and brackets!) Duncan Murdoch Thank you! On Tue, Dec 6, 2011 at 6:22 AM, Duncan Murdochmurdoch.duncan@gmail.**commurdoch.dun...@gmail.com wrote: On 11-12-05 10:32 PM, Michael wrote: Hi all, I am in the middle of debugging which is stopped using browser()... in myfile.R at around line #25. I was then stuck in a big loop which I want to escape and stop the program at the line after the big loop. In the debugging mode, I used Browse[2]setBreakpoint(myfile.R#38) What did it print? I then typed c and ENTER, thinking that it will continue to execute until when it comes across line #38 and then stop there... But it didn't work - it continued the execution until the end of the function, right at the line return(results)... What happened? How to solve this problem? One of the complications in R is that you can have multiple copies of a function in memory. You may (or may not, what did it print??) have set a breakpoint in one copy, then run another. Or you may have edited that function after originally sourcing it, and lost the source reference. An alternative to using setBreakpoint is just to edit a call to browser() into the function. It's less convenient, but more robust. Duncan Murdoch Thanks a lot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**http://www.r-project.org/** posting-guide.htmlhttp://www.**r-project.org/posting-guide.**htmlhttp://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] axis thickness in plot()
On 2011-12-06 08:35, AlexC wrote: Hello, I am trying to increase the thickness of the axis in plot() without reverting to the use of paint programs i see posts on that topic for the xyplot function but want to see if i can do it with plot() because i've already setup my graph script using that i thought i could use axis() function and specify lwd=thickness or lwd.axis= but that does not work like it does for lwd.ticks If anyone has an idea, sincerely heres the script windows(width=7,height=7) plot(data$Winter,data$NbFirstBroods,ylab=number of breeding pairs,xlab=winter harshness,cex=1.5,cex.lab=1.5,cex.axis=1.5,font.axis=2,axes=FALSE) points(data$Winter,data$NbFirstBroods,cex=1.5,col=black,pch=19) abline(lm(data$NbFirstBroods~data$Winter),col=red,lwd=4) Only you have the object you call 'data'. Why not provide a simple example (reproducible and minus the obviously unnecessary annotation) that illustrates your problem? i tried axis(1, lwd.axis = 3,lwd.ticks=3) for example Presumably this gave a warning: lwd.axis is not a graphical parameter. The best thing at that point (if not sooner), is to type ?axis to see what the arguments for that function are. This would immediately show that 'lwd' is the argument you want. also when adding the y axis axis(2...) x and y axes are disconnected Use box() with your choice of bty and lwd. If you want different linewidths for the x and y axes, then retrieve the coordinates of par(usr) and use either abline() or lines(). Peter Ehlers Thank you for your kind help in advance, Alexandre -- View this message in context: http://r.789695.n4.nabble.com/axis-thickness-in-plot-tp4165430p4165430.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] Bootstrapping
Hello,
I am having some trouble setting up a bootstrapping prodecure. I create
artificial data and would like to use these to bootstrap a t-test
statistic from these. Especially I do not really get how boot uses the
indices variable or i variable. Can anybody help out? Thanks!!
b0 - 1/2 # intercept as given
b1 - 1 # slope as given
n - 20 # of rand. numbers
u - rnorm(n, mean=0, sd=1) # generate data
x - rnorm(n, mean=0, sd=1) #
y - b0 + b1*x + u# model
mu - 1
data1 - matrix(, n, 2)# Data from original draw
tval - function(data1, i) {
data1[i,1] - y
data1[i,2] - x
m - lm(data1[,1]~data1[,2])
p - coef(m)[2]
t - (coef(m)[2]-mu)/sqrt(vcov(m)[2,2]) # t-test
t
}
bs - boot(data = data1, statistic = tval, R = 500, sim = ordinary)
bs
ba - boot.array(bs)[1:5,1:10]
ci - boot.ci(bs, conf=0.95, index=1, type=all)
ci.bca - ci$bca[4:5]
plot(bs, index=1)
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Re: [R] Can't load package 'lars'
Hello, I do think so. ### [villandre@stat04 lars]$ pwd /home/villandre/R/x86_64-redhat-linux-gnu-library/2.11/lars [villandre@stat04 lars]$ ls data DESCRIPTION help html INDEX libs Meta NAMESPACE R ### I re-installed it and I still get the same error message. install.packages(lars, lib = ~/R/x86_64-redhat-linux-gnu-library/2.11) trying URL 'http://software.rc.fas.harvard.edu/mirrors/R/src/contrib/lars_0.9-8.tar.gz' Content type 'application/x-gzip' length 172011 bytes (167 Kb) opened URL == downloaded 167 Kb * installing *source* package ‘lars’ ... ** libs gfortran -m64 -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -c delcol.f -o delcol.o gcc -m64 -std=gnu99 -shared -L/usr/local/lib64 -o lars.so delcol.o -lgfortran -lm -L/usr/lib64/R/lib -lR installing to /mnt/prism/s20/villandre/R/x86_64-redhat-linux-gnu-library/2.11/lars/libs ** R ** data ** preparing package for lazy loading ** help *** installing help indices converting help for package ‘lars’ finding HTML links ... done cv.lars html diabeteshtml lars-internal html larshtml plot.lars html predict.larshtml summary.larshtml ** building package indices ... ** testing if installed package can be loaded Loaded lars 0.9-8 * DONE (lars) The downloaded packages are in ‘/tmp/RtmphxCj4j/downloaded_packages’ library(lars, lib.loc = ~/R/x86_64-redhat-linux-gnu-library/2.11) Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for ‘lars’ It is the first time I get such an error message when trying to load a package. It would seem that the problem is with ### cat(Loaded lars, utils::installed.packages()[lars, Version] ### Is there a way to circumvent this problem (e.g. attribute an arbitrary value to utils::installed.packages()[lars, Version])? Thanks for your help, Luc From: Uwe Ligges [lig...@statistik.tu-dortmund.de] Sent: Tuesday, December 06, 2011 8:01 AM To: Luc Villandre Cc: r-help Subject: Re: [R] Can't load package 'lars' On 06.12.2011 03:33, Luc Villandre wrote: Hi, I installed package 'lars' earlier tonight and did not get any sort of error message. ### ** building package indices ... ** testing if installed package can be loaded Loaded lars 0.9-8 * DONE (lars) ### However, when I try to load it, I get ### library(lars, lib.loc = ~/R/x86_64-redhat-linux-gnu-library/2.11) Are you sure it is installed at the location you specified? Uwe Ligges Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for ‘lars’ ### Session info: ### sessionInfo() R version 2.14.0 (2011-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rpart_3.1-50 tools_2.14.0 ### I get the same error message when I try to load it on another machine: ### library(lars,lib.loc = ~/R/i686-pc-linux-gnu-library/2.12) Error : .onLoad failed in loadNamespace() for 'lars', details: call: cat(Loaded lars, utils::installed.packages()[lars, Version], error: subscript out of bounds Error: package/namespace load failed for 'lars' ### Session info: ### sessionInfo() R version 2.13.1 (2011-07-08) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.1 ### Is there at least a way to circumvent the problem? Thank you for your help, Luc Villandre __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] To Try or to TryCatch, I have tried to long
So after about 4 hours struggling with Try and TryCatch I am throwing in the
towel. I have a more complicated function that used logspline through
iterative distributions and at some point the logspline doesnt function
correctly for some subsets but is fine with others so I need to be able to
identify when the error occurs and stop curtailing the distribution and I
think this Try or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 }
}
I would expect this to fail only when i 9 but succeeds each time. DO i
need to specify something different where try-error resides? Thanks guys
Cheers,
Josh
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Re: [R] help! browser() does not get stopped...
yeah, any one line command of checking which function is currently in the memory? so if I find any function not in the .GlobalEnv. then I know what the problem is? 2011/12/6 Uwe Ligges lig...@statistik.tu-dortmund.de On 06.12.2011 18:29, Michael wrote: how do I check and make sure? thx E.g. insert cat(Hello World!\n) in the first line of your function you called subroutine. Best, Uwe Ligges On 12/6/11, Uwe Liggeslig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de wrote: On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! Thanks! __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] help! browser() does not get stopped...
On 06.12.2011 18:45, Michael wrote: yeah, any one line command of checking which function is currently in the memory? Which memory? You have to think about namespaces and environments in such a case, and then, we need to know what you are actually doing. so if I find any function not in the .GlobalEnv. then I know what the problem is? Err, no. So are you working on package and may NAMESPACES be involved or not? If not, my initial guess may be wrong. I think you have to provide more information what you are actually doing and how you did define all your functions that are involved. best, uwe Ligges 2011/12/6 Uwe Liggeslig...@statistik.tu-dortmund.de On 06.12.2011 18:29, Michael wrote: how do I check and make sure? thx E.g. insert cat(Hello World!\n) in the first line of your function you called subroutine. Best, Uwe Ligges On 12/6/11, Uwe Liggeslig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de wrote: On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! Thanks! __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://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] help! browser() does not get stopped...
On 06/12/2011 12:45 PM, Michael wrote: yeah, any one line command of checking which function is currently in the memory? As Uwe said, that's not a very useful thing to do. But if you know the name you're looking for, find() is useful. For example, Browse[1] find(mean) [1] package:base You might also want find(mean, mode=function), in case you've also got a non-function named mean. Duncan Murdoch so if I find any function not in the .GlobalEnv. then I know what the problem is? 2011/12/6 Uwe Liggeslig...@statistik.tu-dortmund.de On 06.12.2011 18:29, Michael wrote: how do I check and make sure? thx E.g. insert cat(Hello World!\n) in the first line of your function you called subroutine. Best, Uwe Ligges On 12/6/11, Uwe Liggeslig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de wrote: On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! Thanks! __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RStudio: copied line is always not the same as the line that I highlighted
Hi all, I am using RStudio. I wanted to copy and past an expression/line. I highlighted it, and then copied and pasted: The result was not the line that I wanted, instead, it was the line above... For example: I have three lines: a b c I highlighted b and copied, but the pasted outcome was a... What happened? Thanks al ot! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to de-source and re-source a file?
i.e. how to make sure the function that was loaded into workspace/memory is the version that I edited latest... not some stale version... This might solve some of my breakpoint and browser/debug problem, even the RStudio problem that I've met thanks a lot! [[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 de-source and re-source a file?
On 06/12/2011 1:10 PM, Michael wrote: i.e. how to make sure the function that was loaded into workspace/memory is the version that I edited latest... not some stale version... This might solve some of my breakpoint and browser/debug problem, even the RStudio problem that I've met You can use rm() to remove a function. You can also quit and restart R, making sure that it *does not* load an existing workspace (by deleting the .Rdata file if it exists, and never answering yes to the question to save it.) This gives you a nice clean slate. 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] help! browser() does not get stopped...
Thanks a lot! What I was wondering is: if we use find, are the results for locally installed packages, or search_paths, or the functions that are loaded into memory? I am looking for some command to tell me which functions are currently in the memory. My understanding is that after the first-run of a function, the function is loaded into memory and stays there until being unloaded. If I don't unload the function, then any newly edited version will not be loaded and the one in memory is the stale version... This might explain a few of my weird problems... Thanks a lot! On Tue, Dec 6, 2011 at 12:04 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 06/12/2011 12:45 PM, Michael wrote: yeah, any one line command of checking which function is currently in the memory? As Uwe said, that's not a very useful thing to do. But if you know the name you're looking for, find() is useful. For example, Browse[1] find(mean) [1] package:base You might also want find(mean, mode=function), in case you've also got a non-function named mean. Duncan Murdoch so if I find any function not in the .GlobalEnv. then I know what the problem is? 2011/12/6 Uwe Liggeslig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de On 06.12.2011 18:29, Michael wrote: how do I check and make sure? thx E.g. insert cat(Hello World!\n) in the first line of your function you called subroutine. Best, Uwe Ligges On 12/6/11, Uwe Liggeslig...@statistik.tu-**d**ortmund.dehttp://dortmund.de/ ligges@statistik.**tu-dortmund.de lig...@statistik.tu-dortmund.de wrote: On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/**posting-guide.html http://www.**r-project.org/posting-guide.**htmlhttp://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-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to de-source and re-source a file?
Thanks a lot! But how about removing all the functions in the whole myprogram1.R source file? The reason for asking this is of course, after I made some changes, I saved it, and then I wanted the functions to be reloaded into memory so that I can do mtrace, or browser etc. Thank you! On Tue, Dec 6, 2011 at 12:17 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 06/12/2011 1:10 PM, Michael wrote: i.e. how to make sure the function that was loaded into workspace/memory is the version that I edited latest... not some stale version... This might solve some of my breakpoint and browser/debug problem, even the RStudio problem that I've met You can use rm() to remove a function. You can also quit and restart R, making sure that it *does not* load an existing workspace (by deleting the .Rdata file if it exists, and never answering yes to the question to save it.) This gives you a nice clean slate. Duncan Murdoch [[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 de-source and re-source a file?
On 06/12/2011 1:19 PM, Michael wrote: Thanks a lot! But how about removing all the functions in the whole myprogram1.R source file? There's no way for R to know what you did with those functions, so no general way to do that. But if you just source it again, it will overwrite the ones in the current evaluation frame. Duncan Murdoch The reason for asking this is of course, after I made some changes, I saved it, and then I wanted the functions to be reloaded into memory so that I can do mtrace, or browser etc. Thank you! On Tue, Dec 6, 2011 at 12:17 PM, Duncan Murdochmurdoch.dun...@gmail.comwrote: On 06/12/2011 1:10 PM, Michael wrote: i.e. how to make sure the function that was loaded into workspace/memory is the version that I edited latest... not some stale version... This might solve some of my breakpoint and browser/debug problem, even the RStudio problem that I've met You can use rm() to remove a function. You can also quit and restart R, making sure that it *does not* load an existing workspace (by deleting the .Rdata file if it exists, and never answering yes to the question to save it.) This gives you a nice clean slate. 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] help! browser() does not get stopped...
On 06/12/2011 1:17 PM, Michael wrote: Thanks a lot! What I was wondering is: if we use find, are the results for locally installed packages, or search_paths, or the functions that are loaded into memory? It finds what get() would find, so that starts with the current evaluation frame, and follows the chain back to the base environment. If you haven't used library() or require() to load a package, it won't be found. I am looking for some command to tell me which functions are currently in the memory. ls() will do that for the current evaluation frame. See its args if you want to search back through the chain. My understanding is that after the first-run of a function, the function is loaded into memory and stays there until being unloaded. That's true, but not relevant. If it hasn't been loaded, a stub is there, and find() will see the stub. If I don't unload the function, then any newly edited version will not be loaded and the one in memory is the stale version... That's not true. As soon as you assign a new value to the name, it will be replaced. But you need to do the assignment in the right place in the chain. Duncan Murdoch This might explain a few of my weird problems... Thanks a lot! On Tue, Dec 6, 2011 at 12:04 PM, Duncan Murdochmurdoch.dun...@gmail.comwrote: On 06/12/2011 12:45 PM, Michael wrote: yeah, any one line command of checking which function is currently in the memory? As Uwe said, that's not a very useful thing to do. But if you know the name you're looking for, find() is useful. For example, Browse[1] find(mean) [1] package:base You might also want find(mean, mode=function), in case you've also got a non-function named mean. Duncan Murdoch so if I find any function not in the .GlobalEnv. then I know what the problem is? 2011/12/6 Uwe Liggeslig...@statistik.tu-**dortmund.delig...@statistik.tu-dortmund.de On 06.12.2011 18:29, Michael wrote: how do I check and make sure? thx E.g. insert cat(Hello World!\n) in the first line of your function you called subroutine. Best, Uwe Ligges On 12/6/11, Uwe Liggeslig...@statistik.tu-**d**ortmund.dehttp://dortmund.de/ ligges@statistik.**tu-dortmund.delig...@statistik.tu-dortmund.de wrote: On 06.12.2011 18:06, Michael wrote: It's weird! I am sure that I have inserted browser() in a sub-routine where I wanted to stop and debug... But when I start running the main function from the separate main file, it doesn't stop within the target sub-routine at all. Probably you are using some package and call the subroutine within the NAMESPACE of the package rather than the one in .GlobalEnv. Uwe Ligges Please help me! Thanks! __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-helphttps://stat.ethz.ch/mailman/**listinfo/r-help https://stat.**ethz.ch/mailman/listinfo/r-**helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/**posting-guide.html http://www.**r-project.org/posting-guide.**htmlhttp://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-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.htmlhttp://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] To Try or to TryCatch, I have tried to long
I think the problem is that it's only a warning and not an error.
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
cat('fail',i,'\n')
result_[[i]]-0 } else {
#If sqrt succeeds
cat('succeed',i,'\n')
result_[[i]] - 1 }
}
result_
On Tue, Dec 6, 2011 at 11:11 AM, LCOG1 jr...@lcog.org wrote:
So after about 4 hours struggling with Try and TryCatch I am throwing in
the
towel. I have a more complicated function that used logspline through
iterative distributions and at some point the logspline doesnt function
correctly for some subsets but is fine with others so I need to be able to
identify when the error occurs and stop curtailing the distribution and I
think this Try or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 }
}
I would expect this to fail only when i 9 but succeeds each time. DO i
need to specify something different where try-error resides? Thanks guys
Cheers,
Josh
--
View this message in context:
http://r.789695.n4.nabble.com/To-Try-or-to-TryCatch-I-have-tried-to-long-tp4165578p4165578.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
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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] convert p-values into z-scores
Is there a program to convert p-values into z-scores for meta-analysis purpose? 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] read.table performance
** Disclaimer: I'm looking for general suggestions **
I'm sorry, but can't send out the file I'm using, so there is no
reproducible example.
I'm using read.table and it's taking over 30 seconds to read a tiny file.
The strange thing is that it takes roughly the same amount of time if the
file is 100 times larger.
After re-reviewing the data Import / Export manual I think the best
approach would be to use Python, or perhaps the readLines function, but I
was hoping to understand why the simple read.table approach wasn't working
as expected.
Some relevant facts:
1. There are about 3700 columns. Maybe this is the problem? Still the
file size is not very large.
2. The file encoding is ANSI, but I'm not specifying that in the
function. Setting fileEncoding=ANSI produces an unsupported conversion
error
3. readLines imports the lines quickly
4. scan imports the file quickly also
Obviously, scan and readLines would require more coding to identify
columns, etc.
my code:
system.time(dat - read.table('C:/test.txt', nrows=-1, sep='\t',
header=TRUE))
It's taking 33.4 seconds and the file size is only 315 kb!
Thanks
Gene
[[alternative HTML version deleted]]
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Find x value of density plots
Hello All, How do I find the x value at max density for say, this plot plot(density(rnorm(1000))) Thank you, P [[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 de-source and re-source a file?
the problem with restarting R is that I then have to re-execute the program until the point where I wanted to debug, which is a very long-waiting time... On Tue, Dec 6, 2011 at 12:17 PM, Duncan Murdoch murdoch.dun...@gmail.comwrote: On 06/12/2011 1:10 PM, Michael wrote: i.e. how to make sure the function that was loaded into workspace/memory is the version that I edited latest... not some stale version... This might solve some of my breakpoint and browser/debug problem, even the RStudio problem that I've met You can use rm() to remove a function. You can also quit and restart R, making sure that it *does not* load an existing workspace (by deleting the .Rdata file if it exists, and never answering yes to the question to save it.) This gives you a nice clean slate. Duncan Murdoch [[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] Find x value of density plots
?density ... and pay attention to the Value details. -- Bert On Tue, Dec 6, 2011 at 10:42 AM, Pavan G pavan.n...@gmail.com wrote: Hello All, How do I find the x value at max density for say, this plot plot(density(rnorm(1000))) Thank you, P [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Bert Gunter Genentech Nonclinical Biostatistics Internal Contact Info: Phone: 467-7374 Website: http://pharmadevelopment.roche.com/index/pdb/pdb-functional-groups/pdb-biostatistics/pdb-ncb-home.htm __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Find x value of density plots
On 06/12/2011 1:42 PM, Pavan G wrote: Hello All, How do I find the x value at max density for say, this plot plot(density(rnorm(1000))) d - density(rnorm(1000)) plot(d) abline(v=d$x[which.max(d$y)]) 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] convert p-values into z-scores
Try this: pval - 0.05 qnorm(1 - (pval/2)) Jean Amidou N'Diaye wrote on 12/06/2011 12:27:25 PM: Is there a program to convert p-values into z-scores for meta-analysis purpose? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] split date nad time
I can't replicate this: does it occur in a fresh R session (no GUI, just straight --vanilla)? If so, sessionInfo()? On Tue, Dec 6, 2011 at 11:23 AM, threshold r.kozar...@gmail.com wrote: ok, dput(AggDateTime[960:962]) structure(c(1314313140L, 1314313200L, 1314313260L), class = c(POSIXct, POSIXt), tzone = ) -- View this message in context: http://r.789695.n4.nabble.com/split-date-nad-time-tp4164191p4165378.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] Sequential Sum in R
I am trying to code the following excel formula in R. ab cResultFormula 1 10 0.1 #N/A IF(B220,NA(),C2+IF(ISERROR(D1),0,D1)) 2 20 0.2 0.2 IF(B320,NA(),C3+IF(ISERROR(D2),0,D2)) 3 30 0.3 0.5 IF(B420,NA(),C4+IF(ISERROR(D3),0,D3)) 4 40 0.4 0.9 IF(B520,NA(),C5+IF(ISERROR(D4),0,D4)) 5 50 0.5 1.4 IF(B620,NA(),C6+IF(ISERROR(D5),0,D5)) 6 60 0.6 2 IF(B720,NA(),C7+IF(ISERROR(D6),0,D6)) 7 70 0.7 2.7 IF(B820,NA(),C8+IF(ISERROR(D7),0,D7)) 8 80 0.8 3.5 IF(B920,NA(),C9+IF(ISERROR(D8),0,D8)) 9 90 0.9 4.4 IF(B1020,NA(),C10+IF(ISERROR(D9),0,D9)) 10100 1 5.4 IF(B1120,NA(),C11+IF(ISERROR(D10),0,D10)) The variable Result is obtained using the excel formula shown next to it. Column D contains the Result. dataFrame - data.frame(a = seq(1:10),b = seq(10,100,by = 10),c = seq(0.1,1,by = 0.1)) Can someone please help me as how to calculate the sequential sum in R given by the excel formula?? Thank you. Ravi -- View this message in context: http://r.789695.n4.nabble.com/Sequential-Sum-in-R-tp4165916p4165916.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] To Try or to TryCatch, I have tried to long
I've had the same problem in other cases.
Does anyone know how to catch warnings as well as errors?
On Tue, Dec 6, 2011 at 12:34 PM, ROLL Josh F jr...@lcog.org wrote:
**
Agreed. But what I am trying to control is when I get a warning. I want
to do something different if a warning OR an error pop up? Any ideas?
Cheers
--
*From:* gley...@gmail.com [mailto:gley...@gmail.com] *On Behalf Of *Gene
Leynes
*Sent:* Tuesday, December 06, 2011 10:27 AM
*To:* ROLL Josh F
*Cc:* r-help@r-project.org
*Subject:* Re: [R] To Try or to TryCatch, I have tried to long
I think the problem is that it's only a warning and not an error.
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
cat('fail',i,'\n')
result_[[i]]-0 } else {
#If sqrt succeeds
cat('succeed',i,'\n')
result_[[i]] - 1 }
}
result_
On Tue, Dec 6, 2011 at 11:11 AM, LCOG1 jr...@lcog.org wrote:
So after about 4 hours struggling with Try and TryCatch I am throwing in
the
towel. I have a more complicated function that used logspline through
iterative distributions and at some point the logspline doesnt function
correctly for some subsets but is fine with others so I need to be able to
identify when the error occurs and stop curtailing the distribution and I
think this Try or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 }
}
I would expect this to fail only when i 9 but succeeds each time. DO i
need to specify something different where try-error resides? Thanks
guys
Cheers,
Josh
--
View this message in context:
http://r.789695.n4.nabble.com/To-Try-or-to-TryCatch-I-have-tried-to-long-tp4165578p4165578.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] read.table performance
On Tue, Dec 6, 2011 at 1:15 PM, Gene Leynes gley...@gmail.com wrote:
** Disclaimer: I'm looking for general suggestions **
I'm sorry, but can't send out the file I'm using, so there is no
reproducible example.
I'm using read.table and it's taking over 30 seconds to read a tiny file.
The strange thing is that it takes roughly the same amount of time if the
file is 100 times larger.
After re-reviewing the data Import / Export manual I think the best
approach would be to use Python, or perhaps the readLines function, but I
was hoping to understand why the simple read.table approach wasn't working
as expected.
Some relevant facts:
1. There are about 3700 columns. Maybe this is the problem? Still the
file size is not very large.
2. The file encoding is ANSI, but I'm not specifying that in the
function. Setting fileEncoding=ANSI produces an unsupported conversion
error
3. readLines imports the lines quickly
4. scan imports the file quickly also
Obviously, scan and readLines would require more coding to identify
columns, etc.
my code:
system.time(dat - read.table('C:/test.txt', nrows=-1, sep='\t',
header=TRUE))
It's taking 33.4 seconds and the file size is only 315 kb!
You could also try read.csv.sql in the sqldf package and see whether
or not that is any faster. Be sure you are using RSQLite 0.11.0 (and
not an earlier version) with that since earlier versions were compiled
to work with only a maximum of 999 columns.
library(sqldf)
DF - read.csv.sql(C:\\test.txt, header = TRUE, sep = \t)
You may or may not have to use the eol= argument to specify line
endings. See ?read.csv.sql
--
Statistics Software Consulting
GKX Group, GKX Associates Inc.
tel: 1-877-GKX-GROUP
email: ggrothendieck at gmail.com
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Sequential Sum in R
vioravis wrote on 12/06/2011 12:42:35 PM: I am trying to code the following excel formula in R. ab cResultFormula 1 10 0.1 #N/A IF(B220,NA(),C2+IF(ISERROR(D1),0,D1)) 2 20 0.2 0.2 IF(B320,NA(),C3+IF(ISERROR(D2),0,D2)) 3 30 0.3 0.5 IF(B420,NA(),C4+IF(ISERROR(D3),0,D3)) 4 40 0.4 0.9 IF(B520,NA(),C5+IF(ISERROR(D4),0,D4)) 5 50 0.5 1.4 IF(B620,NA(),C6+IF(ISERROR(D5),0,D5)) 6 60 0.6 2 IF(B720,NA(),C7+IF(ISERROR(D6),0,D6)) 7 70 0.7 2.7 IF(B820,NA(),C8+IF(ISERROR(D7),0,D7)) 8 80 0.8 3.5 IF(B920,NA(),C9+IF(ISERROR(D8),0,D8)) 9 90 0.9 4.4 IF(B1020,NA(),C10+IF(ISERROR(D9),0,D9)) 10100 1 5.4 IF(B1120,NA(),C11+IF(ISERROR(D10),0,D10)) The variable Result is obtained using the excel formula shown next to it. Column D contains the Result. dataFrame - data.frame(a = seq(1:10),b = seq(10,100,by = 10),c = seq(0.1,1,by = 0.1)) Can someone please help me as how to calculate the sequential sum in R given by the excel formula?? Thank you. Ravi Try this: d - ifelse(dataFrame$b 20, 0, dataFrame$c) dataFrame$result - cumsum(d) dataFrame$result[dataFrame$b 20] - NA Jean [[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] To Try or to TryCatch, I have tried to long
Look at the archives of this mailing list for a discussion
entitled 'Stack trace?' on Nov 9-10 of this year.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Gene Leynes
Sent: Tuesday, December 06, 2011 10:58 AM
To: ROLL Josh F
Cc: r-help@r-project.org
Subject: Re: [R] To Try or to TryCatch, I have tried to long
I've had the same problem in other cases.
Does anyone know how to catch warnings as well as errors?
On Tue, Dec 6, 2011 at 12:34 PM, ROLL Josh F jr...@lcog.org wrote:
**
Agreed. But what I am trying to control is when I get a warning. I want
to do something different if a warning OR an error pop up? Any ideas?
Cheers
--
*From:* gley...@gmail.com [mailto:gley...@gmail.com] *On Behalf Of *Gene
Leynes
*Sent:* Tuesday, December 06, 2011 10:27 AM
*To:* ROLL Josh F
*Cc:* r-help@r-project.org
*Subject:* Re: [R] To Try or to TryCatch, I have tried to long
I think the problem is that it's only a warning and not an error.
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
cat('fail',i,'\n')
result_[[i]]-0 } else {
#If sqrt succeeds
cat('succeed',i,'\n')
result_[[i]] - 1 }
}
result_
On Tue, Dec 6, 2011 at 11:11 AM, LCOG1 jr...@lcog.org wrote:
So after about 4 hours struggling with Try and TryCatch I am throwing in
the
towel. I have a more complicated function that used logspline through
iterative distributions and at some point the logspline doesnt function
correctly for some subsets but is fine with others so I need to be able to
identify when the error occurs and stop curtailing the distribution and I
think this Try or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 }
}
I would expect this to fail only when i 9 but succeeds each time. DO i
need to specify something different where try-error resides? Thanks
guys
Cheers,
Josh
--
View this message in context:
http://r.789695.n4.nabble.com/To-Try-or-to-TryCatch-I-have-tried-to-long-tp4165578p4165578.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] To Try or to TryCatch, I have tried to long
Or, Google for 'R catching warnings' and third entry is the excellent
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of William Dunlap
Sent: Tuesday, December 06, 2011 11:38 AM
To: gleyne...@gmail.com; ROLL Josh F
Cc: r-help@r-project.org
Subject: Re: [R] To Try or to TryCatch, I have tried to long
Look at the archives of this mailing list for a discussion
entitled 'Stack trace?' on Nov 9-10 of this year.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of Gene Leynes
Sent: Tuesday, December 06, 2011 10:58 AM
To: ROLL Josh F
Cc: r-help@r-project.org
Subject: Re: [R] To Try or to TryCatch, I have tried to long
I've had the same problem in other cases.
Does anyone know how to catch warnings as well as errors?
On Tue, Dec 6, 2011 at 12:34 PM, ROLL Josh F jr...@lcog.org wrote:
**
Agreed. But what I am trying to control is when I get a warning. I want
to do something different if a warning OR an error pop up? Any ideas?
Cheers
--
*From:* gley...@gmail.com [mailto:gley...@gmail.com] *On Behalf Of *Gene
Leynes
*Sent:* Tuesday, December 06, 2011 10:27 AM
*To:* ROLL Josh F
*Cc:* r-help@r-project.org
*Subject:* Re: [R] To Try or to TryCatch, I have tried to long
I think the problem is that it's only a warning and not an error.
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
cat('fail',i,'\n')
result_[[i]]-0 } else {
#If sqrt succeeds
cat('succeed',i,'\n')
result_[[i]] - 1 }
}
result_
On Tue, Dec 6, 2011 at 11:11 AM, LCOG1 jr...@lcog.org wrote:
So after about 4 hours struggling with Try and TryCatch I am throwing in
the
towel. I have a more complicated function that used logspline through
iterative distributions and at some point the logspline doesnt function
correctly for some subsets but is fine with others so I need to be able
to
identify when the error occurs and stop curtailing the distribution and I
think this Try or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 }
}
I would expect this to fail only when i 9 but succeeds each time. DO
i
need to specify something different where try-error resides? Thanks
guys
Cheers,
Josh
--
View this message in context:
http://r.789695.n4.nabble.com/To-Try-or-to-TryCatch-I-have-tried-to-long-tp4165578p4165578.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] help wrapping findInterval into a function
On Dec 6, 2011, at 11:43 AM, Steve E. wrote:
Dear R Community,
I hope you might be able to assist with a small problem creating a
function.
I am working with water-quality data sets that contain the
concentration of
many different elements in water samples. I need to assign quality-
control
flags to values that fall into various concentration ranges. Rather
than a
web of nested if statements, I am employing the findInterval
function to
identify values that need to be flagged and to assign the
appropriate flag.
It's probably your use of with rather than findInterval. The 'with'
function sets up an environment and is used mostly in interactive
session. If you have not passed a dataframe into the function then you
should use the name of the dataframe and '['.
The data consist of a sample identifier, the analysis, and
corresponding
value. The findInterval function works well; however, I would like to
incorporate it into a function so that I can run multiple findInterval
functions for many different water-quality analyses (and I have to
do this
for many dataset) but it seems to fall apart when incorporated into a
function.
Run straighforward, the findInterval function works as desired, e.g.
below,
creating the new CalciumFlag column with the appropriate flag for,
in this
case, levels of calcium in the water:
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
However, it does not worked when wrapped in a function (no error
messages
are thrown, it simply does not seem to do anything):
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
}
Calling the function WQfunc() does not produce an error but also
does not
produce the expected CalciumFlag, it seems to not do anything.
Ultimately, what I need to get to is something like below where
multiple
findInterval functions for different analyses are included in a single
function, then I can concatenate the results into a single column
containing
all flags for all analyses, e.g.:
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
WQdata$SodiumFlag - with(WQdata, ifelse(analysis == Sodium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.050,
0.125, 125,
Inf))]),))
WQdata$MagnesiumFlag - with(WQdata, ifelse(analysis ==
Magnesium, (flags
- c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.065,
0.15, 75,
Inf))]),))
.etc for additional water-quality analyses...
}
As an aside, I started working with the findInterval tool from an
example
that I found online but am not clear as to how the multi-component
configuration incorporating brackets actually works, can anyone
suggest a
good resource that explains this?
I thank you very much for any assistance you may be able to provide.
Regards,
Steve
--
View this message in context:
http://r.789695.n4.nabble.com/help-wrapping-findInterval-into-a-function-tp4165464p4165464.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
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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] varaince explined of a regression tree using ctree
Dear, I would like know the way to calculate the variance explained of a regression tree. I use the function ctree from library party many thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RStudio: copied line is always not the same as the line that I highlighted
RStudio is not R. Go ask the RStudio support people at www.rstudio.org. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Michael comtech@gmail.com wrote: Hi all, I am using RStudio. I wanted to copy and past an expression/line. I highlighted it, and then copied and pasted: The result was not the line that I wanted, instead, it was the line above... For example: I have three lines: a b c I highlighted b and copied, but the pasted outcome was a... What happened? Thanks al ot! [[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] To Try or to TryCatch, I have tried to long
Thank for the links. I reread one I found yesterday about changing the
options parameter to options(warn = 2) and that allows the try() function to
see a warning the same way as an error so problem solved using the existing
code.
Cheers,
Josh
-Original Message-
From: William Dunlap [mailto:wdun...@tibco.com]
Sent: Tuesday, December 06, 2011 11:42 AM
To: gleyne...@gmail.com; ROLL Josh F
Cc: r-help@r-project.org
Subject: RE: [R] To Try or to TryCatch, I have tried to long
Or, Google for 'R catching warnings' and third entry is the excellent
http://www.stats.uwo.ca/faculty/murdoch/software/debuggingR/
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of William Dunlap
Sent: Tuesday, December 06, 2011 11:38 AM
To: gleyne...@gmail.com; ROLL Josh F
Cc: r-help@r-project.org
Subject: Re: [R] To Try or to TryCatch, I have tried to long
Look at the archives of this mailing list for a discussion entitled
'Stack trace?' on Nov 9-10 of this year.
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org
[mailto:r-help-boun...@r-project.org] On Behalf Of Gene Leynes
Sent: Tuesday, December 06, 2011 10:58 AM
To: ROLL Josh F
Cc: r-help@r-project.org
Subject: Re: [R] To Try or to TryCatch, I have tried to long
I've had the same problem in other cases.
Does anyone know how to catch warnings as well as errors?
On Tue, Dec 6, 2011 at 12:34 PM, ROLL Josh F jr...@lcog.org wrote:
**
Agreed. But what I am trying to control is when I get a warning.
I want to do something different if a warning OR an error pop up? Any
ideas?
Cheers
--
*From:* gley...@gmail.com [mailto:gley...@gmail.com] *On Behalf Of
*Gene Leynes
*Sent:* Tuesday, December 06, 2011 10:27 AM
*To:* ROLL Josh F
*Cc:* r-help@r-project.org
*Subject:* Re: [R] To Try or to TryCatch, I have tried to long
I think the problem is that it's only a warning and not an error.
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
cat('fail',i,'\n')
result_[[i]]-0 } else {
#If sqrt succeeds
cat('succeed',i,'\n')
result_[[i]] - 1 }
}
result_
On Tue, Dec 6, 2011 at 11:11 AM, LCOG1 jr...@lcog.org wrote:
So after about 4 hours struggling with Try and TryCatch I am
throwing in the towel. I have a more complicated function that
used logspline through iterative distributions and at some point
the logspline doesnt function correctly for some subsets but is
fine with others so I need to be able to identify when the error
occurs and stop curtailing the distribution and I think this Try
or TryCatch should do the trick but I think I am missing
something here. A simple example
result_-list()
for(i in 1:10){
if(inherits(try(sqrt(9-i),silent=TRUE),try-error)){
#If sqrt fails
result_[[i]]-0 } else {
#If sqrt succeeds
result_[[i]] - 1 } }
I would expect this to fail only when i 9 but succeeds each time. DO
i
need to specify something different where try-error resides? Thanks
guys
Cheers,
Josh
--
View this message in context:
http://r.789695.n4.nabble.com/To-Try-or-to-TryCatch-I-have-tried-to-long-tp4165578p4165578.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] making changes to global variables in functions
I'm trying to write a function that takes several objects with many
different attributes and then changes their attributes. So what I wanted to
happen in the simplified example below is for the function to change the
attributes of the objects state1 and state2 that are passed to it. But
because stateA and stateB are local, this isn't working. Are there any easy
solutions?
e.g., if I could combine the two objects stateA and stateB into a single
object, I could return it and then assign it back to objects state1 and
state2. Or if I could pass a pointer to the original object.. But I cannot
find an easy way of doing either. Thanks in advance..
state1 - list(n=100, won=0)
state2 - list(n=100, won=0)
fight2 - function(stateA, stateB){
stateA$n - 50
stateB$n -50
}
fight2(state1,state2)
state1$n
state2$n
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Writing out in loops
Thanks for the reply. I'm writing data out as it is generated into a number of
different files and not saving it as I go (although I could - not sure which
would be quicker). In fact I tried this today and the approach with the loop
seems to run reasonably fast.
Thomas
On 6 Dec 2011, at 15:07, Sarah Goslee wrote:
Is there some reason you can't create the entire file in R and then write it
out in a single step?
It looks like you're writing out
mat[1, 1:10]
so you could just use
write.table(mat[1, 1:10], filen)
Can you expand on what you're trying to do?
Sarah
On Tue, Dec 6, 2011 at 4:18 AM, Thomas chesney@gmail.com wrote:
I would like to write some data to different files. I can create the
filename Day1.txt like this:
filen - paste(Day, l, .txt, sep=)
and then I'm using a For loop to write out one row of a matrix, something
like this:
For (j in 1:10)
{
cat(mat[1,j], ,, file=filen, append=TRUE)
}
cat(\n, file=filen, append=TRUE)
but is there a better way to do this?
Thank you,
Thomas
--
Sarah Goslee
http://www.functionaldiversity.org
__
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] help wrapping findInterval into a function
No, the problem is not with with but is
that the OP's did not return the modified
data.frame. He didn't show how the function
was called, but I suspect the usage was like
f0 - function() globalDataFrame$newCol - ...
f0()
where it should have been
f1 - function(dataFrame) {
dataFrame$newCol - ...
dataFrame # return modified dataFrame
}
globalDataFrame - f1(globalDataFrame)
Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com
-Original Message-
From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
Behalf Of David Winsemius
Sent: Tuesday, December 06, 2011 12:05 PM
To: Steve E.
Cc: r-help@r-project.org
Subject: Re: [R] help wrapping findInterval into a function
On Dec 6, 2011, at 11:43 AM, Steve E. wrote:
Dear R Community,
I hope you might be able to assist with a small problem creating a
function.
I am working with water-quality data sets that contain the
concentration of
many different elements in water samples. I need to assign quality-
control
flags to values that fall into various concentration ranges. Rather
than a
web of nested if statements, I am employing the findInterval
function to
identify values that need to be flagged and to assign the
appropriate flag.
It's probably your use of with rather than findInterval. The 'with'
function sets up an environment and is used mostly in interactive
session. If you have not passed a dataframe into the function then you
should use the name of the dataframe and '['.
The data consist of a sample identifier, the analysis, and
corresponding
value. The findInterval function works well; however, I would like to
incorporate it into a function so that I can run multiple findInterval
functions for many different water-quality analyses (and I have to
do this
for many dataset) but it seems to fall apart when incorporated into a
function.
Run straighforward, the findInterval function works as desired, e.g.
below,
creating the new CalciumFlag column with the appropriate flag for,
in this
case, levels of calcium in the water:
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
However, it does not worked when wrapped in a function (no error
messages
are thrown, it simply does not seem to do anything):
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
}
Calling the function WQfunc() does not produce an error but also
does not
produce the expected CalciumFlag, it seems to not do anything.
Ultimately, what I need to get to is something like below where
multiple
findInterval functions for different analyses are included in a single
function, then I can concatenate the results into a single column
containing
all flags for all analyses, e.g.:
WQfunc - function() {
WQdata$CalciumFlag - with(WQdata, ifelse(analysis == Calcium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.027, 0.1,
100,
Inf))]),))
WQdata$SodiumFlag - with(WQdata, ifelse(analysis == Sodium,
(flags -
c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.050,
0.125, 125,
Inf))]),))
WQdata$MagnesiumFlag - with(WQdata, ifelse(analysis ==
Magnesium, (flags
- c(Y, 'Q', , A) [findInterval(WQdata$value, c(-Inf, 0.065,
0.15, 75,
Inf))]),))
.etc for additional water-quality analyses...
}
As an aside, I started working with the findInterval tool from an
example
that I found online but am not clear as to how the multi-component
configuration incorporating brackets actually works, can anyone
suggest a
good resource that explains this?
I thank you very much for any assistance you may be able to provide.
Regards,
Steve
--
View this message in context:
http://r.789695.n4.nabble.com/help-wrapping-findInterval-into-a-
function-tp4165464p4165464.html
Sent from the R help mailing list archive at Nabble.com.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and
Re: [R] varaince explined of a regression tree using ctree
On 12/06/2011 03:05 PM, Antonio Punzon Merino wrote: I would like know the way to calculate the variance explained of a regression tree. I use the function ctree from library party ctree does not provide this information by default, but it is not difficult to calculate: X - matrix(rnorm(100*10),ncol=10) y - X%*%c(rep(2,5),rep(0,5))+rnorm(100) fit - ctree(y~.,data=as.data.frame(X)) r - y - predict(fit) 1-var(r)/var(y) -- Patrick Breheny Assistant Professor Department of Biostatistics Department of Statistics University of Kentucky __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] using StatEt IDE for Eclipse
Hi, I'm trying to use StatEt IDE for Eclipse as my R editor, but I'm completely lost. I've read all I could find online, made apparently all I had to do (installing rj, configuraing StatEt, etc.) but still cannot make R running. Below is the error log file. Thank you so much for assistance. Matteo !ENTRY de.walware.statet.r.console.ui 1 0 2011-12-05 16:21:51.355 !MESSAGE Launching the R Console was cancelled, because it seems starting the R engine failed. Please make sure that R package 'rj' (1.0.0 or compatible) is installed and that the R library paths are set correctly for the R environment configuration 'R-2.14.0'. !SESSION 2011-12-05 16:23:23.552 --- eclipse.buildId=M20110909-1335 java.version=1.6.0_21 java.vendor=Sun Microsystems Inc. BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=it_IT Command-line arguments: -os win32 -ws win32 -arch x86_64 !ENTRY org.eclipse.osgi 2 1 2011-12-05 16:23:29.901 !MESSAGE NLS unused message: FindReplaceAction_label in: de.walware.ecommons.ui.SharedMessages !ENTRY org.eclipse.ui 4 4 2011-12-05 16:23:30.712 !MESSAGE Class load Failure: 'org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem' !ENTRY org.eclipse.ui 4 0 2011-12-05 16:23:30.714 !MESSAGE Class load Failure: 'org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem' !STACK 1 org.eclipse.core.runtime.CoreException: Plug-in de.walware.ecommons.ltk.ui was unable to load class org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem. at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194) at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:176) at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905) at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243) at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55) at org.eclipse.ui.internal.util.Util.safeLoadExecutableExtension(Util.java:879) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.createContributionItem(DynamicMenuContributionItem.java:222) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.getContributionItem(DynamicMenuContributionItem.java:215) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.fill(DynamicMenuContributionItem.java:195) at org.eclipse.jface.action.MenuManager.doItemFill(MenuManager.java:741) at org.eclipse.jface.action.MenuManager.update(MenuManager.java:822) at org.eclipse.jface.action.MenuManager.update(MenuManager.java:682) at org.eclipse.ui.internal.menus.WorkbenchMenuService.updateManagers(WorkbenchMenuService.java:330) at org.eclipse.ui.internal.menus.WorkbenchMenuService$4.propertyChange(WorkbenchMenuService.java:316) at org.eclipse.ui.internal.services.EvaluationAuthority$1.run(EvaluationAuthority.java:252) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at org.eclipse.ui.internal.services.EvaluationAuthority.fireServiceChange(EvaluationAuthority.java:246) at org.eclipse.ui.internal.services.EvaluationAuthority.endSourceChange(EvaluationAuthority.java:197) at org.eclipse.ui.internal.services.EvaluationAuthority.sourceChanged(EvaluationAuthority.java:135) at org.eclipse.ui.internal.services.ExpressionAuthority.sourceChanged(ExpressionAuthority.java:311) at org.eclipse.ui.internal.services.ExpressionAuthority.sourceChanged(ExpressionAuthority.java:290) at org.eclipse.ui.AbstractSourceProvider.fireSourceChanged(AbstractSourceProvider.java:99) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkActivePart(WorkbenchSourceProvider.java:401) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkActivePart(WorkbenchSourceProvider.java:300) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.handleCheck(WorkbenchSourceProvider.java:286) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkOtherSources(WorkbenchSourceProvider.java:855) at org.eclipse.ui.internal.services.WorkbenchSourceProvider$6.handleEvent(WorkbenchSourceProvider.java:839) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84) at org.eclipse.swt.widgets.Display.filterEvent(Display.java:1262) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1052) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1077) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1058) at org.eclipse.swt.widgets.Decorations.WM_ACTIVATE(Decorations.java:1647) at org.eclipse.swt.widgets.Shell.WM_ACTIVATE(Shell.java:2137) at org.eclipse.swt.widgets.Control.windowProc(Control.java:4525) at org.eclipse.swt.widgets.Canvas.windowProc(Canvas.java:341) at org.eclipse.swt.widgets.Decorations.windowProc(Decorations.java:1610) at org.eclipse.swt.widgets.Shell.windowProc(Shell.java:2061) at
Re: [R] making changes to global variables in functions
No pointer functionality in R (that I know of), but if you want to
return two objects as one the standard way is to put them in a list
and to return that list.
Michael
On Tue, Dec 6, 2011 at 2:35 PM, Yev kirp...@gmail.com wrote:
I'm trying to write a function that takes several objects with many
different attributes and then changes their attributes. So what I wanted to
happen in the simplified example below is for the function to change the
attributes of the objects state1 and state2 that are passed to it. But
because stateA and stateB are local, this isn't working. Are there any easy
solutions?
e.g., if I could combine the two objects stateA and stateB into a single
object, I could return it and then assign it back to objects state1 and
state2. Or if I could pass a pointer to the original object.. But I cannot
find an easy way of doing either. Thanks in advance..
state1 - list(n=100, won=0)
state2 - list(n=100, won=0)
fight2 - function(stateA, stateB){
stateA$n - 50
stateB$n -50
}
fight2(state1,state2)
state1$n
state2$n
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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-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/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] using StatEt IDE for Eclipse
You will likely find more help on the StatEt mailing list, since the author of the package monitors it: http://lists.r-forge.r-project.org/mailman/listinfo/statet-user On Tue, Dec 6, 2011 at 4:04 PM, Matteo Richiardi matteo.richia...@gmail.com wrote: Hi, I'm trying to use StatEt IDE for Eclipse as my R editor, but I'm completely lost. I've read all I could find online, made apparently all I had to do (installing rj, configuraing StatEt, etc.) but still cannot make R running. Below is the error log file. Thank you so much for assistance. Matteo !ENTRY de.walware.statet.r.console.ui 1 0 2011-12-05 16:21:51.355 !MESSAGE Launching the R Console was cancelled, because it seems starting the R engine failed. Please make sure that R package 'rj' (1.0.0 or compatible) is installed and that the R library paths are set correctly for the R environment configuration 'R-2.14.0'. !SESSION 2011-12-05 16:23:23.552 --- eclipse.buildId=M20110909-1335 java.version=1.6.0_21 java.vendor=Sun Microsystems Inc. BootLoader constants: OS=win32, ARCH=x86_64, WS=win32, NL=it_IT Command-line arguments: -os win32 -ws win32 -arch x86_64 !ENTRY org.eclipse.osgi 2 1 2011-12-05 16:23:29.901 !MESSAGE NLS unused message: FindReplaceAction_label in: de.walware.ecommons.ui.SharedMessages !ENTRY org.eclipse.ui 4 4 2011-12-05 16:23:30.712 !MESSAGE Class load Failure: 'org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem' !ENTRY org.eclipse.ui 4 0 2011-12-05 16:23:30.714 !MESSAGE Class load Failure: 'org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem' !STACK 1 org.eclipse.core.runtime.CoreException: Plug-in de.walware.ecommons.ltk.ui was unable to load class org.eclipse.ecf.docshare.menu.DocShareRosterMenuContributionItem. at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.throwException(RegistryStrategyOSGI.java:194) at org.eclipse.core.internal.registry.osgi.RegistryStrategyOSGI.createExecutableExtension(RegistryStrategyOSGI.java:176) at org.eclipse.core.internal.registry.ExtensionRegistry.createExecutableExtension(ExtensionRegistry.java:905) at org.eclipse.core.internal.registry.ConfigurationElement.createExecutableExtension(ConfigurationElement.java:243) at org.eclipse.core.internal.registry.ConfigurationElementHandle.createExecutableExtension(ConfigurationElementHandle.java:55) at org.eclipse.ui.internal.util.Util.safeLoadExecutableExtension(Util.java:879) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.createContributionItem(DynamicMenuContributionItem.java:222) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.getContributionItem(DynamicMenuContributionItem.java:215) at org.eclipse.ui.internal.menus.DynamicMenuContributionItem.fill(DynamicMenuContributionItem.java:195) at org.eclipse.jface.action.MenuManager.doItemFill(MenuManager.java:741) at org.eclipse.jface.action.MenuManager.update(MenuManager.java:822) at org.eclipse.jface.action.MenuManager.update(MenuManager.java:682) at org.eclipse.ui.internal.menus.WorkbenchMenuService.updateManagers(WorkbenchMenuService.java:330) at org.eclipse.ui.internal.menus.WorkbenchMenuService$4.propertyChange(WorkbenchMenuService.java:316) at org.eclipse.ui.internal.services.EvaluationAuthority$1.run(EvaluationAuthority.java:252) at org.eclipse.core.runtime.SafeRunner.run(SafeRunner.java:42) at org.eclipse.ui.internal.services.EvaluationAuthority.fireServiceChange(EvaluationAuthority.java:246) at org.eclipse.ui.internal.services.EvaluationAuthority.endSourceChange(EvaluationAuthority.java:197) at org.eclipse.ui.internal.services.EvaluationAuthority.sourceChanged(EvaluationAuthority.java:135) at org.eclipse.ui.internal.services.ExpressionAuthority.sourceChanged(ExpressionAuthority.java:311) at org.eclipse.ui.internal.services.ExpressionAuthority.sourceChanged(ExpressionAuthority.java:290) at org.eclipse.ui.AbstractSourceProvider.fireSourceChanged(AbstractSourceProvider.java:99) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkActivePart(WorkbenchSourceProvider.java:401) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkActivePart(WorkbenchSourceProvider.java:300) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.handleCheck(WorkbenchSourceProvider.java:286) at org.eclipse.ui.internal.services.WorkbenchSourceProvider.checkOtherSources(WorkbenchSourceProvider.java:855) at org.eclipse.ui.internal.services.WorkbenchSourceProvider$6.handleEvent(WorkbenchSourceProvider.java:839) at org.eclipse.swt.widgets.EventTable.sendEvent(EventTable.java:84) at org.eclipse.swt.widgets.Display.filterEvent(Display.java:1262) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1052) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1077) at org.eclipse.swt.widgets.Widget.sendEvent(Widget.java:1058) at
Re: [R] Change the limits of a plot a posteriori
The zoomplot function in the TeachingDemos package can be used for this (it actually redoes the entire plot, but with new limits). This will generally work for a quick exploration, but for quality plots it is suggested to create the 1st plot with the correct range to begin with. -- 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-bounces@r- project.org] On Behalf Of jcano Sent: Thursday, December 01, 2011 11:12 AM To: r-help@r-project.org Subject: [R] Change the limits of a plot a posteriori Hi all How can I change the limits (xlim or ylim) in a plot that has been already created? For example, consider this naive example curve(dbeta(x,2,4)) curve(dbeta(x,8,13),add=T,col=2) When adding the second curve, it goes off the original limits computed by R for the first graph, which are roughly, c(0,2.1) I know two obvious solutions for this, which are: 1) passing a sufficiently large parameter e.g. ylim=c(0,4) to the first graphic curve(dbeta(x,2,4),ylim=c(0,4)) curve(dbeta(x,8,13),add=T,col=2) or 2) switch the order in which I plot the curves curve(dbeta(x,8,13),col=2) curve(dbeta(x,2,4),add=T) but I guess if there is any way of adjusting the limits of the graphic a posteriori, once you have a plot with the undesired limits, forcing R to redraw it with the new limits, but without having to execute again the curve commands Hope I made myself clear Best regards and thank you very much in advance -- View this message in context: http://r.789695.n4.nabble.com/Change-the- limits-of-a-plot-a-posteriori-tp4129750p4129750.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] any R-Revolution users here? How to make Revolution portable?
How to make a portable version of Revolution R? I just wanted to be able to carry it anywhere I go in a USB drive... I don't need fancy functionalities, just need the visual debugger therein... btw, Windows or Linux doesn't matter... Any thoughts? Thanks a lot! [[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.
