Re: [R] Problem Installign Packages
On Aug 16, 2012, at 8:48 PM, ziad.elmou...@tnsglobal.com wrote: To Whom It May Concern, In attempting to install the e1071 package, I get the message below after selecting the mirror site. And what was the command you issued? -- Please select a CRAN mirror for use in this session --- Warning: unable to access index for repository http://mirror.fcaglp.unlp.edu.ar/CRAN/bin/windows/contrib/2.15 I seem to have the problem with any other package that I attempt to install. Please advise. Use a different mirror (or that mirror may have been down and will now work.) -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] specific matrix element tranformation
Hello,
Inline
Em 17-08-2012 04:39, bantex escreveu:
Hi guys,
After a long while I came up with this :
set.seed(2)
a-matrix(rnorm(4),ncol=2)
abc-function(a)
{
b=matrix(NA,nrow=3,ncol=3)
b[1,1]=a[1,1]+1
b[1,2]=a[2,1]*a[2,2]
b[1,3]=a[2,2]+a[1,1]
b[2,1]=a[1,1]-5
b[2,2]=sqrt(a[2,2])
b[2,3]=a[1,1]/a[2,2]
b[3,1]=a[2,2]-3
b[3,2]=a[1,1]*(a[1,2]+a[2,2])
b[3,3]=sqrt(a[1,1])/a[1,2]
return(b=matrix(c(b[1,1],b[1,2],b[1,3],b[2,1],b[2,2],b[2,3],
b[3,1],b[3,2],b[3,3]),ncol=3))
You don't need to say that 'b' is a matrix a second time! And this form
is wrong, you should add 'byrow = TRUE' since you're using row order.
}
How can I improve on it?
With your data, you would have two errors in applying function abc to
matrix 'a'. Try the following.
fun - function(a){
b - matrix(nrow = 3, ncol = 3)
#let's say these are the transformations i wish to perform
b[1,1] - a[1,1]+1
b[1,2] - a[2,1]*a[2,2]
b[1,3] - a[2,2]+a[1,1]
b[2,1] - a[1,1]-5
if(a[2,2] 0){
warning(a[2, 2] is negative, using zero for its square root
b[2,2].)
b[2,2] - 0
}else{
b[2,2] - sqrt(a[2,2])
}
if(a[2,2] == 0){
warning(a[2, 2] is zero, using zero for division result b[2,3].)
b[2,3] - 0
}else{
b[2,3] - a[1,1]/a[2,2]
}
b[3,1] - a[2,2]-3
b[3,2] - a[1,1]*(a[1,2]+a[2,2])
if(a[1,2] == 0){
warning(a[1, 2] is zero, using zero for division result b[3,3].)
b[3,3] - 0
}else if(a[1,1]/a[1,2] 0){
warning(a[1,1]/a[1,2] is negative, using zero for its square
root b[3,3].)
b[3,3] - 0
}else{
b[3,3] - sqrt(a[1,1]/a[1,2])
}
b
}
set.seed(2)
a - matrix(rnorm(4),ncol = 2)
fun(a)
Cheers,
B
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Re: [R] specific matrix element tranformation
On Aug 16, 2012, at 8:39 PM, bantex wrote:
Hi guys,
After a long while I came up with this :
set.seed(2)
a-matrix(rnorm(4),ncol=2)
abc-function(a)
{
b=matrix(NA,nrow=3,ncol=3)
b[1,1]=a[1,1]+1
b[1,2]=a[2,1]*a[2,2]
b[1,3]=a[2,2]+a[1,1]
b[2,1]=a[1,1]-5
b[2,2]=sqrt(a[2,2])
b[2,3]=a[1,1]/a[2,2]
b[3,1]=a[2,2]-3
b[3,2]=a[1,1]*(a[1,2]+a[2,2])
b[3,3]=sqrt(a[1,1])/a[1,2]
# return(b=matrix(c(b[1,1],b[1,2],b[1,3],b[2,1],b[2,2],b[2,3],
# b[3,1],b[3,2],b[3,3]),ncol=3))
return(b)
}
How can I improve on it?
Cheers,
B
--
View this message in context:
http://r.789695.n4.nabble.com/specific-matrix-element-tranformation-tp4640550p4640554.html
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__
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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.
David Winsemius, MD
Alameda, CA, USA
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] r data structures
To slightly correct what's been said: In general lists are linear objects, but a list can have dimension. An example is in Circle 8.1.8 of 'The R Inferno'. http://www.burns-stat.com/pages/Tutor/R_inferno.pdf Pat On 16/08/2012 21:50, Schumacher, Jay S wrote: are these correct/accurate/sensible statements: a vector is a one dimensional object. a matrix is a two dimensional object. a list is a one dimensional object. i'm working from this web page: http://www.agr.kuleuven.ac.be/vakken/statisticsbyR/someDataStructures.htm - On Aug 16, 2012, at 11:49 AM, Schumacher, Jay S wrote: hi, i'm trying to understand r data structures. i see that vectors, matrix, factors and arrays have a dimension. there seems to be no mention of dimensionality anywhere for lists or dataframes. can i consider lists and frames to be of fixed dimension 2? About half of what you have deduced is wrong. Matrices, arrays, and dataframes do have dimensions, at least in technical R parlance, namely they have an attribute which can be queried with dim(). By definition matrices and dataframes have 2 dimensions. Arrays and matrices can be redimensioned, but dataframes cannot. Factors, lists, and atomic vectors do not have dimensions, but they do have lengths. An appropriately structured list (one with vectors all the same length) can be coerced to a dataframe with as.data.frame(). -- Patrick Burns pbu...@pburns.seanet.com twitter: @portfolioprobe http://www.portfolioprobe.com/blog http://www.burns-stat.com (home of 'Some hints for the R beginner' and 'The R Inferno') __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] impute multilevel data in MICE
Dear list, I have a question about imputing 2 level data in MICE, could you give me some suggestions please? Thank you very much. The data set contains 35634 cases and 1007 variables, 280 of them are categorical variables, and the rest of them are continuous variables. On the second level, there are 198 units. I am trying to impute missing values for 270 categorical variables by using the principle components of all the continuous variables. In the JSS paper about MICE: It requires the specification of the fixed effects, the random effects and the class variable. Furthermore, it assumes that the predictors contain a column of ones representing the intercept. Random effects are coded in the predictor matrix as a `2'. The class variable (only one is allowed) is coded by a `-2'. and R pred[popular, ] - c(0, -2, 0, 2, 1, 2, 0) R imp - mice(popmis, meth = c(, , 2l.norm, , , + , ), pred = pred, maxit = 1, seed = 71152) My questions are: 1. In the above example, only 1 variable have missing values, so in the code, only one 2l.norm was specified. In my case, I have 270 categorical variables to be imputed, how do I do this? 2. how to designate the fixed effects, random effects and class variable in the above code with 2 and -2? 3. Should I add a column myself into the data set with 1 for all values for the intercept term? I already have the unit ID variables in the data set, should I change all the values of it to -2? and what does 0 and 1 in R pred[popular, ] - c(0, -2, 0, 2, 1, 2, 0) mean? 4. Is there any example similar to my situation please? The example in the paper is a quite simple case. Thank you very much. ya [[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] specific matrix element tranformation
Hello,
I've made a mistake, it's in the last if/else/if/else. Complete
statement below.
Em 17-08-2012 06:23, Rui Barradas escreveu:
Hello,
Inline
Em 17-08-2012 04:39, bantex escreveu:
Hi guys,
After a long while I came up with this :
set.seed(2)
a-matrix(rnorm(4),ncol=2)
abc-function(a)
{
b=matrix(NA,nrow=3,ncol=3)
b[1,1]=a[1,1]+1
b[1,2]=a[2,1]*a[2,2]
b[1,3]=a[2,2]+a[1,1]
b[2,1]=a[1,1]-5
b[2,2]=sqrt(a[2,2])
b[2,3]=a[1,1]/a[2,2]
b[3,1]=a[2,2]-3
b[3,2]=a[1,1]*(a[1,2]+a[2,2])
b[3,3]=sqrt(a[1,1])/a[1,2]
return(b=matrix(c(b[1,1],b[1,2],b[1,3],b[2,1],b[2,2],b[2,3],
b[3,1],b[3,2],b[3,3]),ncol=3))
You don't need to say that 'b' is a matrix a second time! And this
form is wrong, you should add 'byrow = TRUE' since you're using row
order.
}
How can I improve on it?
With your data, you would have two errors in applying function abc to
matrix 'a'. Try the following.
fun - function(a){
b - matrix(nrow = 3, ncol = 3)
#let's say these are the transformations i wish to perform
b[1,1] - a[1,1]+1
b[1,2] - a[2,1]*a[2,2]
b[1,3] - a[2,2]+a[1,1]
b[2,1] - a[1,1]-5
if(a[2,2] 0){
warning(a[2, 2] is negative, using zero for its square root
b[2,2].)
b[2,2] - 0
}else{
b[2,2] - sqrt(a[2,2])
}
if(a[2,2] == 0){
warning(a[2, 2] is zero, using zero for division result
b[2,3].)
b[2,3] - 0
}else{
b[2,3] - a[1,1]/a[2,2]
}
b[3,1] - a[2,2]-3
b[3,2] - a[1,1]*(a[1,2]+a[2,2])
if(a[1,2] == 0){
warning(a[1, 2] is zero, using zero for division result
b[3,3].)
b[3,3] - 0
}else if(a[1,1]/a[1,2] 0){
warning(a[1,1]/a[1,2] is negative, using zero for its square
root b[3,3].)
b[3,3] - 0
}else{
b[3,3] - sqrt(a[1,1]/a[1,2])
}
b
}
set.seed(2)
a - matrix(rnorm(4),ncol = 2)
fun(a)
Correction:
if(a[1,2] == 0){
warning(a[1, 2] is zero, using zero for division result b[3,3].)
b[3,3] - 0
}else if(a[1,1] 0){
warning(a[1, 1] is negative, using zero for its square root
b[3,3].)
b[3,3] - 0
}else{
b[3,3] - sqrt(a[1,1])/a[1,2]
}
I thought it was sqrt(a[1,1]/a[1,2]).
And apparently I've also forgot to sign.
Rui Barradas
Cheers,
B
--
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http://www.R-project.org/posting-guide.html
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] multiple boxplots on the same figure - reducing space in between
thanks! this solves my problem perfectly -- View this message in context: http://r.789695.n4.nabble.com/multiple-boxplots-on-the-same-figure-reducing-space-in-between-tp4640503p4640570.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] no true negative data, need roc curve
Okay, first of a point in ROC space is spanned by true positive rate and false positive rate. Now you need to decide if you want to plot a curve for each image or maybe a curve for the complete data (add all together). In your case you only have 2 thresholds, so that makes the curves a little awkward because you only have 4 points total, but whatever. Lets say you want a curve for image1: tp1-1066 fp1-70 fn1-116 tn1-0 tpr1-tp1/(tp1+fn1) fpr1-fp1/(fp1+tn1) tp2-446 fp2-41 fn2-55 tn2-0 tpr2-tp2/(tp2+fn2) fpr2-fp2/(fp2+tn2) plot(0,0,type=n,ylim=c(0,1),xlim=c(0,1)) points(c(0,fpr1,fpr2,1),c(0,tpr1,tpr2,1)) lines(c(0,fpr1,fpr2,1),c(0,tpr1,tpr2,1)) Now i have to say though, after taking a look at that data you provided: THE DATA IS WRONG If you add up all values (tp+tn+fp+fn), the number in threshold 2 is lower than in threshold 1. It needs to be the same, so what the hell have you DONE? ^^ greetings Jessi On 16.08.2012, at 17:49, Jessica Streicher wrote: To clarify: Is TN = 0 or do you not know TN (N)? On 16.08.2012, at 11:51, vjyns wrote: Hi, I want to plot ROC curve for my detection algorithm which detects features in different images at two different thresholds. 6 different images used and obtained tp, fp and fn. No tn in my case. in first threshold run i obtained 6 values of tp,fp and fn. In second threshold run agian i got 6 more. i had calculated tpr and fpr. How to plot ROC in this case. Is this possible to plot ROC curve in this case? If s, please guide me to plot that. thank you. http://r.789695.n4.nabble.com/file/n4640474/in1.png -- View this message in context: http://r.789695.n4.nabble.com/no-true-negative-data-need-roc-curve-tp4640474.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-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 message headers matched a filter rule
Pretty much every time i reply to a post in this list i get a bounce saying the above, + waiting for approval. I first thought it was because i didn't send in plain, but now they are and it hasn't become any better. Any other ideas? Is this normal? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] no true negative data, need roc curve
Hi, thanks for the quick response, but as i said in my case due to two different threshold the detected features will differ. Moreover, there is some standard /refined/ formula in calculating the tpr and fpr. herewith i had attached the refined formula from a standard international journal http://r.789695.n4.nabble.com/file/n4640577/tpr_and_fpr.jpg when i used the above mentioned formula (fpr=fp/fp+tp) then i can able to see my point are distributed on the extreme left corner. Like this it is possible to put all the 6 images. Will you please suggest me now how to obtain the plot for different images of two threshold. -- View this message in context: http://r.789695.n4.nabble.com/no-true-negative-data-need-roc-curve-tp4640474p4640577.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] Get the filename from the given path
Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? - thanks in advance Antony. -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp4640578.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Problem with global variable building a package
Hi, I could build the package, finally, adjusting the path correctly (Rtools folders in front). Regards Eva --- El jue, 16/8/12, Eva Prieto Castro evapcas...@yahoo.es escribió: De: Eva Prieto Castro evapcas...@yahoo.es Asunto: Re: [R] Problem with global variable building a package Para: Uwe Ligges lig...@statistik.tu-dortmund.de CC: Greg Snow 538...@gmail.com, R-help@r-project.org Fecha: jueves, 16 de agosto, 2012 10:50 I forget one question: Where do I indicate this path? : PATH=c:\Rtools\bin;c:\Rtools\gcc-4.6.3\bin;c:\MiKTeX\miktex\bin; c:\R\R-2.15\bin\i386;c:\windows;c:\windows\system32 Regards, Eva --- El jue, 16/8/12, Eva Prieto Castro evapcas...@yahoo.es escribió: De: Eva Prieto Castro evapcas...@yahoo.es Asunto: Re: [R] Problem with global variable building a package Para: Uwe Ligges lig...@statistik.tu-dortmund.de CC: Greg Snow 538...@gmail.com, R-help@r-project.org Fecha: jueves, 16 de agosto, 2012 10:41 Hi, I altered .internal file as Ligges indicated, but I have a problem when I make R CMD build pkg: ERROR packaging into .tar.gz failed The question is the following: what is the problem? I have installed Rtools, Must I do anything else?. Obs.: I work under Windows 7, but the package generated will be used under windows and mac. Thanks in advance. Eva --- El mié, 8/8/12, Uwe Ligges lig...@statistik.tu-dortmund.de escribió: De: Uwe Ligges lig...@statistik.tu-dortmund.de Asunto: Re: [R] Problem with global variable building a package Para: Eva Prieto Castro evapcas...@yahoo.es CC: Greg Snow 538...@gmail.com, R-help@r-project.org Fecha: miércoles, 8 de agosto, 2012 11:24 On 08.08.2012 08:53, Eva Prieto Castro wrote: Hello, Greg: That is one of the solutions I have tried; the problem is that I can't obtain a package in this way, because an glo-internal.R file is generated (glo is the name of the package) and when I try to create the package an error message appears (a parse error). The content of the glo-internal.R file is the following: .glo.env - environment To avoid parser errors, replace environment by something that is syntactically valid, in this case: new.env(). Best, Uwe Ligges where .glo.env is the name of the new environment I create in my source code. What am I doing wrong?. Thanks again for your help. Regards. Eva --- El mar, 7/8/12, Greg Snow 538...@gmail.com escribió: De: Greg Snow 538...@gmail.com Asunto: Re: [R] Problem with global variable building a package Para: Eva Prieto Castro evapcas...@yahoo.es CC: R-help@r-project.org Fecha: martes, 7 de agosto, 2012 23:30 Probably the best thing to do is create an environment within the package that you can assign to and read from. Somewhere in the source code for the package include a line like: my.env - new.env() then within any functions defined after that line you can set variables within the environment with code like: àmy.env$paramA - 3 and other functions can then read my.env$paramA.àThis way you don't need to worry about assign or - and all your functions will have access to the same set of variables (but they won't interfere with the users workspace). On Tue, Aug 7, 2012 at 1:09 AM, Eva Prieto Castro evapcas...@yahoo.es wrote: Hi, My name is Eva and this is my first message here. My English is not very good, but I hope you can understand my question, in the context of an academic project. I have developed several functions in R and the idea is that the user can access functions in order to: 1) Alter parameters in relation with data and type of analysis. 2) Run statistical analysis (Text and pdf files with results will be generated). 3) View the value of the most important parameters. All the parameters I need are stored in a list object, and this list is used in all the functions along the cycle performed by the user, but I would like the user does not need to pass the name of the list as argument when he/she runs the different functions, so I think I need to treat the list as a global variable. Firstly, I used the global assignment operator (ââ¬Å-ââ¬Å); secondly, I used ââ¬Ågetââ¬ï¿½ and ââ¬Åassignââ¬ï¿½ functions and even I used a new.env() in order to use a new environment exclusively for my list. However, when I try to build a package with all my functions I donââ¬â¢t reach this end, because of an error in parse process. My question for you is the following: taking into account that my end is to build a package, what can I do with this ââ¬Åglobalââ¬ï¿½ list?. How can I treat it?. Thanks in advance. Regards, Eva àààà à à [[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,
[R] How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)?
df - data.frame ( RowId = 4:7, x=c(1_1, 2_2, 3_3, 3_3), y=c(1_1, 3_3, 2_2, 3_3) ) How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)? If they were not matced exactly how can we get the row id? In this case the row ids were 5 and 6. Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-6692tel:%2B91-40-6692 and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). [[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 and install old package to R 2.11 in UNIX
On 17.08.2012 02:42, David Winsemius wrote: On Aug 16, 2012, at 4:33 PM, Kevin Goulding wrote: Hi, I'm having trouble installing and using the 'foreign' package in R on a UNIX machine. sessionInfo() R version 2.11.1 (2010-05-31) sparc-sun-solaris2.10 locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base Is there a way to find and install an old 'foreign' package that works with my machine? Does such a method generalize to finding other out-of-date packages for my machine? Yes, there is a general method. Install from archived package as source. http://cran.r-project.org/src/contrib/Archive Right, but then foreign is a recommended package and is shipped with released versions of R, hence should be available already. 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.
Re: [R] How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)?
On 08/17/2012 07:48 PM, Sri krishna Devarayalu Balanagu wrote: df- data.frame ( RowId = 4:7, x=c(1_1, 2_2, 3_3, 3_3), y=c(1_1, 3_3, 2_2, 3_3) ) How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)? If they were not matced exactly how can we get the row id? In this case the row ids were 5 and 6. Hi Sri krishna Devarayalu Balanagu, how about this: df$RowId[which(df$x != df$y)] Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] The message headers matched a filter rule
It happens relatively often to me. Regards Le 17/08/2012 17:19, Jessica Streicher a écrit : Pretty much every time i reply to a post in this list i get a bounce saying the above, + waiting for approval. I first thought it was because i didn't send in plain, but now they are and it hasn't become any better. Any other ideas? Is this normal? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] tikzDevice not available
Hello, many thanks for the advice. Unfortunately I did not mention that my os is Windows 7. I am sorry for that. Some feedback here? install.packages(tikzDevice, repos=http://R-Forge.R-project.org;) Installing package(s) into C:/Users/N31k/Documents/R/win-library/2.14 (as lib is unspecified) Warning: unable to access index for repository http://R-Forge.R-project.org/bin/windows/contrib/2.14 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package tikzDevice is not available (for R version 2.14.2) utils:::menuInstallLocal() Error in read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) : cannot open the connection In addition: Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) : cannot open compressed file 'tikzDevice_0.6.2.tar.gz/DESCRIPTION', probable reason 'No such file or directory' [[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] Trouble compiling package on Windows (64 bit)
I am trying to compile the R package KernGPLM found here: http://www.marlenemueller.de/KernGPLM/KernGPLM_0.65.tar.gz since the binary available is for R 2.4. but the compilation ends with the error message: *** arch-i386 ERROR: compilation failed for the package 'KernGPLM' Here is my session info: R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] Revobase_6.0.0 RevoMods_6.0.0 RevoScaleR_3.0-0 lattice_0.20-0 loaded via a namespace (and not attached): [1] codetools_0.2-8 foreach_1.4.0 grid_2.14.2 iterators_1.0.6 [5] tools_2.14.2 Is it possible to diagnose the problem from this information? 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] Reference a variable inside a string and another for object assingments
On Thu, Aug 16, 2012 at 3:30 PM, Kenneth Rose kennethros...@gmail.com wrote: Hi R community I copied a bit of my R code that gets some data from a database. You won't be able to run the code, but I am a beginner so you will probably understand what going on. I would like to make a variable I can refer to inside the sqlQuery. Instead of writing the start date and time (ex SP.lokaldatotid = '2005-01-01 00:00:00') inside the query I would like to define it in the beginning of the code, so I don't have to fiddle with a lot of dates each time I wan't to change it. I would like to do this for a few of the variables and maybe even make a list/array I can loop through, so I don't have to write the same code multiple times (for SYS and DK1). I have searched for a solution for two days now, but I am not sure what it's called and are probably writing the wrong queries :-) Thank you for your help! Kenneth My code: library(xts) library(RODBC) #Define channnel (i configured my own SYSTEM-DNS, via ODBC) ch - odbcConnect(DI2) # ## GET DATA## # ## SYSTEM spot ## # Hent data fra SQL Server sys - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP, WHERE (SP.omraade_id= 0 AND SP.lokaldatotid = '2005-01-01 00:00:00'))) #Definer dato og tid kolonne sys$lokaldatotid - as.POSIXct(sys$lokaldatotid) #Make a XTS object sys_xts - xts(sys[,-1], order.by=sys[,1]) # Recalculate data from hours to daily, monthly and yearly averages sys_xts_daily - apply.daily(sys_xts, FUN=mean) sys_xts_monthly - apply.monthly(sys_xts, FUN=mean) sys_xts_yearly - apply.yearly(sys_xts, FUN=mean) ## DK1 spot # # Hent data fra SQL Server dk1 - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP, WHERE (SP.omraade_id= 5 AND SP.lokaldatotid = '2005-01-01 00:00:00'))) You can use paste as shown in the example in ?sqlGetResults or fn$ in the gsubfn package can do quasi-perl-like string interpolation. With fn you just preface any command with fn$ and then its arguments are subject to string interpolation as explained further in ?fn and http://gsubfn.googlecode.com. e.g. library(gsubfn) id - 5 date - '2005-01-01 00:00:00' dk1 - fn$sqlQuery (ch, SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP WHERE (SP.omraade_id = $id AND SP.lokaldatotid = '$date' ) ) -- 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] How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)?
Hello, I've changed the name of the data.frame, df is an R function. DF$RowId[ DF$x != DF$y ] Hope this helps, Rui Barradas Em 17-08-2012 10:48, Sri krishna Devarayalu Balanagu escreveu: df - data.frame ( RowId = 4:7, x=c(1_1, 2_2, 3_3, 3_3), y=c(1_1, 3_3, 2_2, 3_3) ) How can we compare corresponding values of x and y (first value of x exacly matches with the first value of y)? If they were not matced exactly how can we get the row id? In this case the row ids were 5 and 6. Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-6692tel:%2B91-40-6692 and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). [[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] tikzDevice not available
On 17.08.2012 12:37, nikos giallousis wrote: Hello, many thanks for the advice. Unfortunately I did not mention that my os is Windows 7. I am sorry for that. Some feedback here? Yes: R-forge seems to support the current release version of R only re. binaries. If you want it for an old release of R, install from sources, i.e.: install.packages(tikzDevice, repos=http://R-Forge.R-project.org;, type=source) Uwe Ligges install.packages(tikzDevice, repos=http://R-Forge.R-project.org;) Installing package(s) into ‘C:/Users/N31k/Documents/R/win-library/2.14’ (as ‘lib’ is unspecified) Warning: unable to access index for repository http://R-Forge.R-project.org/bin/windows/contrib/2.14 Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ‘tikzDevice’ is not available (for R version 2.14.2) utils:::menuInstallLocal() Error in read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) : cannot open the connection In addition: Warning messages: 1: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file 2: In read.dcf(file.path(pkgname, DESCRIPTION), c(Package, Type)) : cannot open compressed file 'tikzDevice_0.6.2.tar.gz/DESCRIPTION', probable reason 'No such file or directory' [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error in metafor documentation on maximum iterations
At 19:01 16/08/2012, Viechtbauer Wolfgang (STAT) wrote: I had noticed this oversight a while ago. In an updated version of the metafor package (hopefully to be released in the near future), the argument will be called maxiter (as intended). Using maxit will then work as well, due to partial matching. Thanks for bringing this to my attention though. Also, the package name is metafor (spelled with an f). It's supposed to be a (convoluted) abbreviation for META-analysis FOr R). I suppose metaphor would then be META-analysis PHOr R, but I decided against that (other candidates were metaforR, metafoR, and a few others). Well, at the time, I thought the name metafor was clever. These days, I am not so sure anymore. The big advantage of metafor is that it is not the (English) word for metaphor so making Google searching for metafor a lot easier (at least from my location). Readers in the Nordic countries mileage probably varies here. Best, Wolfgang -- Wolfgang Viechtbauer, Ph.D., Statistician Department of Psychiatry and Psychology School for Mental Health and Neuroscience Faculty of Health, Medicine, and Life Sciences Maastricht University, P.O. Box 616 (VIJV1) 6200 MD Maastricht, The Netherlands +31 (43) 388-4170 | http://www.wvbauer.com -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Michael Weylandt Sent: Thursday, August 16, 2012 04:19 To: John Hodgson Cc: r-help@r-project.org Subject: Re: [R] Error in metafor documentation on maximum iterations Send this to Wolfgang directly. See maintainer(metaphor) Michael On Aug 15, 2012, at 12:13 PM, John Hodgson j...@formby.plus.com wrote: Both the official R documentation and Wolfgang's paper in the Journal of Statistical Science describing this (extremely useful) package, name the control variable for maximum iterations in numeric model fitting as 'maxiter'. The correct name is 'maxit'. A small point concerning an (I guess) infrequently used bit of functionality, but this may help save someone an hour or so's head scratching! John Hodgson __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. Michael Dewey i...@aghmed.fsnet.co.uk http://www.aghmed.fsnet.co.uk/home.html __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Linear mixed model using R
Thanks, Bert. 2012/8/17 Bert Gunter gunter.ber...@gene.com 1. Post on R-sig-mixed-models, not here. 2. Models 2 and 3 make no sense (to me, anyway). What do you think they mean? (Don't answer here -- explain on the mixed models list). -- Bert On Thu, Aug 16, 2012 at 9:13 PM, li li hannah@gmail.com wrote: Dear all, I am trying to use R to fit mixed models. Take the following example, where ind is a random effect and sample is fixed. I wanted to fit Model 1: values = ind + sample Model 2: values =ind * sample Model 3: values=ind(sample) + sample Tried to use the below for mod1, but it did not work. Can anyone give some help on this. Thanks so much. mod1 - lme(values ~ sample + random=~ 1|ind, data=y) Your syntax is wrong. Re-read ?lme (random is a separate argument, not part of the formula). values ind sample 1 0.03325 1 1 2 0.03305 1 1 3 0.03185 1 1 4 0.03515 1 1 5 0.03375 1 1 6 0.01180 1 2 7 0.01850 1 3 8 0.02915 1 4 9 0.06200 1 5 10 0.03230 2 1 11 0.03345 2 1 12 0.03385 2 1 13 0.03605 2 1 14 0.03225 2 1 15 0.01145 2 2 16 0.01805 2 3 17 0.02950 2 4 18 0.05995 2 5 19 0.03425 3 1 20 0.03575 3 1 21 0.03535 3 1 22 0.03380 3 1 23 0.03410 3 1 24 0.01050 3 2 25 0.01735 3 3 26 0.03140 3 4 27 0.06170 3 5 28 0.03430 4 1 29 0.03185 4 1 30 0.03165 4 1 31 0.03380 4 1 32 0.03235 4 1 33 0.01100 4 2 34 0.01825 4 3 35 0.03045 4 4 36 0.06060 4 5 [[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.htmlhttp://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 [[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] Trouble compiling package on Windows (64 bit)
On 17.08.2012 12:38, Fg Nu wrote: I am trying to compile the R package KernGPLM found here: http://www.marlenemueller.de/KernGPLM/KernGPLM_0.65.tar.gz since the binary available is for R 2.4. but the compilation ends with the error message: *** arch-i386 ERROR: compilation failed for the package 'KernGPLM' See the R Installation and Administration manual. It tells you how to set up an environment under Windows to be able to install the package from sources. We cannot say more without the actual output of R CMD INSTALL. Best, Uwe Ligges Here is my session info: R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] Revobase_6.0.0 RevoMods_6.0.0 RevoScaleR_3.0-0 lattice_0.20-0 loaded via a namespace (and not attached): [1] codetools_0.2-8 foreach_1.4.0 grid_2.14.2 iterators_1.0.6 [5] tools_2.14.2 Is it possible to diagnose the problem from this information? 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] Get the filename from the given path
On Fri, Aug 17, 2012 at 5:28 AM, Rantony antony.akk...@ge.com wrote: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? Quite possibly by yelling at it or regular expressions: you know, whatever - thanks in advance Antony. -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp4640578.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] Get the filename from the given path
On Fri, Aug 17, 2012 at 5:28 AM, Rantony antony.akk...@ge.com wrote: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? Please don't shout. ?basename Berend __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get the filename from the given path
-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 17/08/12 15:04, Berend Hasselman wrote: On Fri, Aug 17, 2012 at 5:28 AM, Rantony antony.akk...@ge.com wrote: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? Please don't shout. Just to explain - not everybody knows this: writing in capital letters is considered as shouting in emails and in forums, and not used to highlight certain parts. Cheers, Rainer ?basename Berend -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAlAuTpQACgkQoYgNqgF2egqDSwCePmmZ7blv4vlwqF8ANufs13x8 YccAnA+eqjGmueHlOup083/WfSbNP7RL =McDs -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] Plot multiple variables: label points
Hello, I have a data.frame with 10-15 entries which looks like this: group time1 time2 time3 1 F18 4394.500 21043.50 14949.00 2 F25 4678.000 23727.65 15683.12 3 F30 4909.775 23487.60 16724.40 I plot this with: plot(variable[,2:4]) so that a plot with 3 rows and 3 lines for time1, time2 and time3 appears. Is it somehow possible to label the data points with the values stored in group (F18, F25...)? -- View this message in context: http://r.789695.n4.nabble.com/Plot-multiple-variables-label-points-tp4640611.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] no true negative data, need roc curve
Above mentioned formula is wrong - maybe a typo http://en.wikipedia.org/wiki/Receiver_operating_characteristic The false positive rate is the rate of false positives, meaning how many of the total negatives (all in reality negatives(N), that is, all negatives falsely classified as positives(fp) and all negatives correctly classified as negatives(tn)) have been falsely classified as positive. Also the authors obviously had (N+P=number of features), and therefore at least could have computed this properly. For example: N+P=100 P=TP+FN N=FP+TN - do the math with what you got On 17.08.2012, at 11:13, vjyns wrote: Hi, thanks for the quick response, but as i said in my case due to two different threshold the detected features will differ. Moreover, there is some standard /refined/ formula in calculating the tpr and fpr. herewith i had attached the refined formula from a standard international journal http://r.789695.n4.nabble.com/file/n4640577/tpr_and_fpr.jpg when i used the above mentioned formula (fpr=fp/fp+tp) then i can able to see my point are distributed on the extreme left corner. Like this it is possible to put all the 6 images. Will you please suggest me now how to obtain the plot for different images of two threshold. -- View this message in context: http://r.789695.n4.nabble.com/no-true-negative-data-need-roc-curve-tp4640474p4640577.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] Reference a variable inside a string and another for object assingments
I tried these two and testquery2 now does the job :) Somehow the str_c
function from the stringr package doesn't work when I run the sqlQuery
function even though the testquery string is the same as testquery2
string. Thanks for the pointers!
fromdate - c('2005-01-01 00:00:00')
testquery - str_c(SELECT SP.lokaldatotid, SP.pris FROM
DataIndsamling2.dbo.SpotPriser SP,
WHERE (SP.omraade_id= 0 AND SP.lokaldatotid =
,fromdate[1],))
testquery2 - paste(SELECT SP.lokaldatotid, SP.pris FROM
DataIndsamling2.dbo.SpotPriser SP,
WHERE (SP.omraade_id= 0 AND SP.lokaldatotid =
,fromdate[1],))
I still can't figure out how to assign an existing xts object to a
name from a list or array. I have data that i want to rename to one of
the names i a character vector.
Example:
names - c(data2, data3)
data - xts(11:10, Sys.Date()+1:10)
# The next part is not real code but just so you get the basic idea:
names[1] - data
remove(data)
data2 should now be assigned to data.
Thanks for your help with the first part!!
/Kenneth
On Thu, Aug 16, 2012 at 10:57 PM, MacQueen, Don macque...@llnl.gov wrote:
I sometimes do this sort of thing with tricks like this:
sql - select * from mytable where dt = 'ADATE'
dbGetQuery( con, gsub('ADATE', '2012-06-12 23:14', sql) )
Or if mydates is a vector of dates stored as a POSIXt object:
for (id in mydates) {
dbGetQuery( con, gsub('ADATE', format(id), sql) )
}
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 8/16/12 12:30 PM, Kenneth Rose kennethros...@gmail.com wrote:
Hi R community
I copied a bit of my R code that gets some data from a database. You
won't be able to run the code, but I am a beginner so you will
probably understand what going on.
I would like to make a variable I can refer to inside the sqlQuery.
Instead of writing the start date and time (ex SP.lokaldatotid =
'2005-01-01 00:00:00') inside the query I would like to define it in
the beginning of the code, so I don't have to fiddle with a lot of
dates each time I wan't to change it. I would like to do this for a
few of the variables and maybe even make a list/array I can loop
through, so I don't have to write the same code multiple times (for
SYS and DK1).
I have searched for a solution for two days now, but I am not sure
what it's called and are probably writing the wrong queries :-)
Thank you for your help!
Kenneth
My code:
library(xts)
library(RODBC)
#Define channnel (i configured my own SYSTEM-DNS, via ODBC)
ch - odbcConnect(DI2)
#
## GET DATA##
#
## SYSTEM spot ##
# Hent data fra SQL Server
sys - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM
DataIndsamling2.dbo.SpotPriser SP,
WHERE (SP.omraade_id= 0 AND
SP.lokaldatotid = '2005-01-01 00:00:00')))
#Definer dato og tid kolonne
sys$lokaldatotid - as.POSIXct(sys$lokaldatotid)
#Make a XTS object
sys_xts - xts(sys[,-1], order.by=sys[,1])
# Recalculate data from hours to daily, monthly and yearly averages
sys_xts_daily - apply.daily(sys_xts, FUN=mean)
sys_xts_monthly - apply.monthly(sys_xts, FUN=mean)
sys_xts_yearly - apply.yearly(sys_xts, FUN=mean)
## DK1 spot #
# Hent data fra SQL Server
dk1 - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM
DataIndsamling2.dbo.SpotPriser SP,
WHERE (SP.omraade_id= 5 AND
SP.lokaldatotid = '2005-01-01 00:00:00')))
#Definer dato og tid kolonne
dk1$lokaldatotid - as.POSIXct(dk1$lokaldatotid)
#Lav om til xts object
dk1_xts - xts(dk1[,-1], order.by=dk1[,1])
#Data omregnet fra time - daglig, måned, årlige gennemsnit
dk1_xts_daily - apply.daily(dk1_xts, FUN=mean)
dk1_xts_monthly - apply.monthly(dk1_xts, FUN=mean)
dk1_xts_yearly - apply.yearly(dk1_xts, FUN=mean)
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Re: [R] Reference a variable inside a string and another for object assingments
Thanks Gabor! This is exactly what I was searching for! --- And it works like a charm. On Fri, Aug 17, 2012 at 1:03 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Thu, Aug 16, 2012 at 3:30 PM, Kenneth Rose kennethros...@gmail.com wrote: Hi R community I copied a bit of my R code that gets some data from a database. You won't be able to run the code, but I am a beginner so you will probably understand what going on. I would like to make a variable I can refer to inside the sqlQuery. Instead of writing the start date and time (ex SP.lokaldatotid = '2005-01-01 00:00:00') inside the query I would like to define it in the beginning of the code, so I don't have to fiddle with a lot of dates each time I wan't to change it. I would like to do this for a few of the variables and maybe even make a list/array I can loop through, so I don't have to write the same code multiple times (for SYS and DK1). I have searched for a solution for two days now, but I am not sure what it's called and are probably writing the wrong queries :-) Thank you for your help! Kenneth My code: library(xts) library(RODBC) #Define channnel (i configured my own SYSTEM-DNS, via ODBC) ch - odbcConnect(DI2) # ## GET DATA## # ## SYSTEM spot ## # Hent data fra SQL Server sys - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP, WHERE (SP.omraade_id= 0 AND SP.lokaldatotid = '2005-01-01 00:00:00'))) #Definer dato og tid kolonne sys$lokaldatotid - as.POSIXct(sys$lokaldatotid) #Make a XTS object sys_xts - xts(sys[,-1], order.by=sys[,1]) # Recalculate data from hours to daily, monthly and yearly averages sys_xts_daily - apply.daily(sys_xts, FUN=mean) sys_xts_monthly - apply.monthly(sys_xts, FUN=mean) sys_xts_yearly - apply.yearly(sys_xts, FUN=mean) ## DK1 spot # # Hent data fra SQL Server dk1 - sqlQuery (ch, paste(SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP, WHERE (SP.omraade_id= 5 AND SP.lokaldatotid = '2005-01-01 00:00:00'))) You can use paste as shown in the example in ?sqlGetResults or fn$ in the gsubfn package can do quasi-perl-like string interpolation. With fn you just preface any command with fn$ and then its arguments are subject to string interpolation as explained further in ?fn and http://gsubfn.googlecode.com. e.g. library(gsubfn) id - 5 date - '2005-01-01 00:00:00' dk1 - fn$sqlQuery (ch, SELECT SP.lokaldatotid, SP.pris FROM DataIndsamling2.dbo.SpotPriser SP WHERE (SP.omraade_id = $id AND SP.lokaldatotid = '$date' ) ) -- 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] Get the filename from the given path
Hello, basename(FPath) Hope this helps, Rui Barradas Em 17-08-2012 10:28, Rantony escreveu: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? - thanks in advance Antony. -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp4640578.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] Get the filename from the given path
Thanks pramod. From: Pramod [via R] [mailto:ml-node+s789695n4640600...@n4.nabble.com] Sent: Friday, August 17, 2012 5:24 PM To: Akkara, Antony (GE Energy, Non-GE) Subject: Re: Get the filename from the given path x - substr(FPath,13,nchar(FPath)) should give you the desired output. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp464 0578p4640600.html To unsubscribe from Get the filename from the given path, click here http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscrib e_by_codenode=4640578code=YW50b255LmFra2FyYUBnZS5jb218NDY0MDU3OHwxNTUx OTQzMDI5 . NAML http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_view erid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.Bas icNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.tem plate.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml -instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemai l.naml -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp4640578p4640601.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Get the filename from the given path
On 17.08.2012 11:28, Rantony wrote: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? basename(FPath) Uwe Ligges - thanks in advance Antony. -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp4640578.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] Get the filename from the given path
Do splits - strsplit(filePath,file://%22,fixed=true)[[1/]] fileName - splits[length(splits)]) [[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] Unequal splits from a column
HI, Try this: dat1-data.frame(slope=c(slope (60/25/15),slope (90/10),slope (40/35/15/10),slope (40/25/25/10) )) dat1$slope-gsub(slope\\s+.*(\\(.*\\)),\\1,dat1$slope) dat1$slope-gsub(\\((.*)\\),\\1,dat1$slope) dat2-strsplit(dat1$slope,/) dat2[[1]][4]-0 dat2[[2]][3:4]-0 data.frame(do.call(rbind,dat2)) # X1 X2 X3 X4 #1 60 25 15 0 #2 90 10 0 0 #3 40 35 15 10 #4 40 25 25 10 - Original Message - From: Sapana Lohani lohani.sap...@ymail.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Friday, August 17, 2012 1:05 AM Subject: [R] Unequal splits from a column Hi I am new to R so am struggling with the commands here I have one column in a table that looks like slope (60/25/15) slope (90/10) slope (40/35/15/10) slope (40/25/25/10) I want to have 4 columns with just the number inside the parenthesis. when there is no number that cell can have 0. I want the output like this 60 25 15 0 90 10 0 0 40 35 15 10 40 25 25 10 Can somebody help me?? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error: level sets of factors are different?
Why the error is coming? even though the length of outcome.new$compkey and outcome.new$armkey were exactly same. Can anyone help? setwd(D:/AZ) library(RODBC) cdb_cnct - odbcConnectExcel(AZIF_DC_GVK_NSCLC_MSALL_287papers_02072012_141450_v1_4.xls) outcomes - sqlFetch(cdb_cnct, Outcomes_info) odbcClose(cdb_cnct) rm(cdb_cnct) sink(Dependency checks.log) outcomes[(outcomes$Comparator != ), ] - outcome compkey - paste(outcome$Comparator, outcome$Comparator_Subarm, sep='_') armkey - paste(outcome$Arm_ID, outcome$SubArm_ID, sep='_') outcome.new - cbind(outcome, compkey, armkey) invalid.ids - outcome.new[outcome.new$compkey == outcome.new$armkey, c(Assessment_record_ID)] Error in Ops.factor(outcome.new$compkey, outcome.new$armkey) : level sets of factors are different Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-6692tel:%2B91-40-6692 and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). [[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] dimnames in an array(I'll be grateful if this message will be passed to all list users)
Michael, Thank you for suggestions; it seems to me that there's a fundamental lacuna with respect to names of a three dimensional array: that is, rownames fits dimension 1, colnames fits another dimension(that is, 3, if I read it correctly), but there is no specific name for the third dimension. I've tried setnames thinking that this would be appropriate for naming the sets, but there is no such R function. On the other hand you're right, the suggestion             dimnames(data11a)[[2]]=c(V,R) doesn't ameliorate the analysis: while now dimnames(data11a)[[2]] comes out as [2] returning to the original analysis the same error comes up, that is, that the length of dimnames[2] doesn't agree with thee. 'array extent' -- that is, even though the boxcar contents are two in number, it evaluates the analysis on the basis of the dimnames(data11a)[2] value. I'm using colloc infer (available under R 2.14) and trying to do the FHN(FitzHugh Nagumo) analysis in section 9.1 of the manual; it's very complex work, but I doubt the program is in error. It seems to me in any case that, if R demands that the length of 'dimnames[2] must be equal to the array extent, then there must be a way to make the length of the names equal to the extent of the array, am I right? Otherwise R would be inconsistent with itself, like Nomad on Startrek, and I've never seen a case where it was thus. This is again why I ask if others with extensive experience with dimnames of an array have seen anything similar. Certainly someone might know what is the significance of the dimnames of the array, how much can the length of them be altered for use generally? regards, A Thu, 16 Aug 2012 00:00:35 -0400 Ð¾Ñ R. Michael Weylandt michael.weyla...@gmail.com: On Wed, Aug 15, 2012 at 3:57 AM, aleksandr shfets a_shf...@mail.ru wrote: Hi Michael, Thanks for help on double brackets: I wasn't aware of this use of them. I went back to readjust my array so the dimnames(data11a)[[2]] would have two elements, and remade the array to include the new dimnames: dimnames(data11a)[[2]]=c(V,R) so that inside the second car of the train would be two items? Yes. There seems to be no way to define dimnames(data11a)[2] to be two elements rather than one[as you say we have no way to combine the elements of the train except using the train]. You could do this: dimnames(data11a)[2] - list(c(V,R)) but I'm not sure that's any clearer. To keep the metaphor rolling (get it!), list() puts your stuff in a boxcar so now you can put it directly on the train. So having tried to do what I can to make the middle element of the list to two rather than one, I rerun the analysis with the same result. if I read the thing right, regardless of how I define the inside of the boxcar, the analysis that I referred to res11a = inneropt(coefs, times=times, data=data11a, lik=lik, proc=proc, pars=spars, in.meth='nlminb', control.in=control.out) Where is this inneropt function from? It could be an error in that. If it's from a package, give me the name and I'll take a look at it and you can also contact the maintainer: get contact info using the maintainer() function. Also, some of the advice here will probably be helpful in seeking follow-up: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example Cheers, Michael still won't look at the 'contents' of the car, but gives the same message: Error in `colnames-`(`*tmp*`, value = c(V, R)) : length of 'dimnames' [2] not equal to array extent I've tried a couple of other things like, after defining the second boxcar as: dimnames(data11a)[[2]]=c(V,R) then dimnames(data11a)[2]=list(dimnames(data11a)[[2]]) but this last generates an error. Somehow I think that that the clue to the thing is in the error message: what I see[ with my untrained eye] is that there should be some way to reconcile the three-- colnames, dimnames and the array- to a greater degree than their present agreement. Am I right? regards, Russell Tue, 14 Aug 2012 01:27:50 -0400 Ð¾Ñ R. Michael Weylandt michael.weyla...@gmail.com: On Mon, Aug 13, 2012 at 5:10 AM, aleksandr russell sss...@gmail.com wrote: Hello, I'm hoping someone with a wide experience with R may be able to see what the program is trying to tell me. I've got an array: y1=rnorm(41,0.2) y2=rnorm(41,0.2) y3=rbind(y1,y2) data11-array(0,c(41,2,2)) data11[,1,]=y3 data11[,2,]=y3 rownames(data11)-rownames(data11, do.NULL = FALSE, prefix = Obs.) colnames=c(V,R) varnames=c(one,two) dimnames(data11)-list(rownames(data11), varnames, colnames) data11a-as.array(data11, dimnames=dimnames(data11))
Re: [R] Plot multiple variables: label points
?text Have you read the Introduction to R tutorial. If not, do so before further posting. If so, re-read section 12.2. -- Bert On Fri, Aug 17, 2012 at 6:33 AM, cm256 d-...@gmx.at wrote: Hello, I have a data.frame with 10-15 entries which looks like this: group time1 time2 time3 1 F18 4394.500 21043.50 14949.00 2 F25 4678.000 23727.65 15683.12 3 F30 4909.775 23487.60 16724.40 I plot this with: plot(variable[,2:4]) so that a plot with 3 rows and 3 lines for time1, time2 and time3 appears. Is it somehow possible to label the data points with the values stored in group (F18, F25...)? -- View this message in context: http://r.789695.n4.nabble.com/Plot-multiple-variables-label-points-tp4640611.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. -- 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] How to join two plotmath type expressions
On Aug 15, 2012, at 23:17 , Trevor Carey-Smith wrote: On 08/15/2012 10:45 PM, S Ellison wrote: label- 'Temperature' unit- bquote(degree*C) text(5,5,substitute(l~u, list(l=label, u=unit))) Thanks, that's exactly what I was after. A curious application of bquote though. How about using it where it matters? plot(5, 4) label - 'Temperature' unit - quote(degree*C) text(5, 5, bquote(.(label) ~ .(unit))) Regards, Trevor. -- Please consider the environment before printing this email. NIWA is the trading name of the National Institute of Water Atmospheric Research Ltd. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dimnames in an array(I'll be grateful if this message will be passed to all list users)
Have you showed us how to reproduce your original problem? Have you showed us the output of traceback() after encountering the error? Have you tried setting options(error=recover) before encountering the error and then using recover() to look at the dimensions and dimnames of the array that caused the problem? This error message Error in `colnames-`(`*tmp*`, value = c(V, R)) : length of 'dimnames' [2] not equal to array extent comes from a nested replacement operation. One such such case is mat - matrix(1:6,nrow=2,ncol=3) colnames(mat)[1:2] - c(V, R) where the nested replacement gets expanded into tmp - colnames(mat) # tmp becomes NULL tmp[1:2] - c(V, R) # tmp becomes c(V,R), length is 2 colnames(tmp) - tmp # error: 2 colnames for 3 columns (R uses `*tmp*` where I used tmp - the former is for internal use only.) There are lots of other possibilities, but you need to at least show the output of traceback() to pin it down. 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 aleksandr shfets Sent: Friday, August 17, 2012 6:25 AM To: R. Michael Weylandt Cc: r-help@r-project.org Subject: Re: [R] dimnames in an array(I'll be grateful if this message will be passed to all list users) Michael, Thank you for suggestions; it seems to me that there's a fundamental lacuna with respect to names of a three dimensional array: that is, rownames fits dimension 1, colnames fits another dimension(that is, 3, if I read it correctly), but there is no specific name for the third dimension. I've tried setnames thinking that this would be appropriate for naming the sets, but there is no such R function. On the other hand you're right, the suggestion dimnames(data11a)[[2]]=c(V,R) doesn't ameliorate the analysis: while now dimnames(data11a)[[2]] comes out as [2] returning to the original analysis the same error comes up, that is, that the length of dimnames[2] doesn't agree with thee. 'array extent' -- that is, even though the boxcar contents are two in number, it evaluates the analysis on the basis of the dimnames(data11a)[2] value. I'm using colloc infer (available under R 2.14) and trying to do the FHN(FitzHugh Nagumo) analysis in section 9.1 of the manual; it's very complex work, but I doubt the program is in error. It seems to me in any case that, if R demands that the length of 'dimnames[2] must be equal to the array extent, then there must be a way to make the length of the names equal to the extent of the array, am I right? Otherwise R would be inconsistent with itself, like Nomad on Startrek, and I've never seen a case where it was thus. This is again why I ask if others with extensive experience with dimnames of an array have seen anything similar. Certainly someone might know what is the significance of the dimnames of the array, how much can the length of them be altered for use generally? regards, A Thu, 16 Aug 2012 00:00:35 -0400 от R. Michael Weylandt michael.weyla...@gmail.com: On Wed, Aug 15, 2012 at 3:57 AM, aleksandr shfets a_shf...@mail.ru wrote: Hi Michael, Thanks for help on double brackets: I wasn't aware of this use of them. I went back to readjust my array so the dimnames(data11a)[[2]] would have two elements, and remade the array to include the new dimnames: dimnames(data11a)[[2]]=c(V,R) so that inside the second car of the train would be two items? Yes. There seems to be no way to define dimnames(data11a)[2] to be two elements rather than one[as you say we have no way to combine the elements of the train except using the train]. You could do this: dimnames(data11a)[2] - list(c(V,R)) but I'm not sure that's any clearer. To keep the metaphor rolling (get it!), list() puts your stuff in a boxcar so now you can put it directly on the train. So having tried to do what I can to make the middle element of the list to two rather than one, I rerun the analysis with the same result. if I read the thing right, regardless of how I define the inside of the boxcar, the analysis that I referred to res11a = inneropt(coefs, times=times, data=data11a, lik=lik, proc=proc, pars=spars, in.meth='nlminb', control.in=control.out) Where is this inneropt function from? It could be an error in that. If it's from a package, give me the name and I'll take a look at it and you can also contact the maintainer: get contact info using the maintainer() function. Also, some of the advice here will probably be helpful in seeking follow-up: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible- example Cheers,
Re: [R] Get the filename from the given path
On Aug 17, 2012, at 10:00 AM, Rainer M Krug r.m.k...@gmail.com wrote: -BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 17/08/12 15:04, Berend Hasselman wrote: On Fri, Aug 17, 2012 at 5:28 AM, Rantony antony.akk...@ge.com wrote: Hi, Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? Please don't shout. Just to explain - not everybody knows this: writing in capital letters is considered as shouting in emails and in forums, and not used to highlight certain parts. Cheers, Rainer Thanks Rainer: for the OP, this is also a good read for those getting acquainted with mailing lists http://www.catb.org/esr/faqs/smart-questions.html Michael ?basename Berend -BEGIN PGP SIGNATURE- Version: GnuPG v1.4.11 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/ iEYEARECAAYFAlAuTpQACgkQoYgNqgF2egqDSwCePmmZ7blv4vlwqF8ANufs13x8 YccAnA+eqjGmueHlOup083/WfSbNP7RL =McDs -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. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Error: level sets of factors are different?
The length of a vector of yes/no answers has little to do with the number of possible responses (2). Factors keep both pieces of information. If you only have yes responses in your data set, when converted to factor you would have to tell R that other responses were possible. I prefer to avoid working with factors until I need them. Use the str function to investigate where factors are being introduced and either use options to keep the data as character or convert it back to character if you can't figure that out. --- 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. Sri krishna Devarayalu Balanagu balanagudevaray...@gvkbio.com wrote: Why the error is coming? even though the length of outcome.new$compkey and outcome.new$armkey were exactly same. Can anyone help? setwd(D:/AZ) library(RODBC) cdb_cnct - odbcConnectExcel(AZIF_DC_GVK_NSCLC_MSALL_287papers_02072012_141450_v1_4.xls) outcomes - sqlFetch(cdb_cnct, Outcomes_info) odbcClose(cdb_cnct) rm(cdb_cnct) sink(Dependency checks.log) outcomes[(outcomes$Comparator != ), ] - outcome compkey - paste(outcome$Comparator, outcome$Comparator_Subarm, sep='_') armkey - paste(outcome$Arm_ID, outcome$SubArm_ID, sep='_') outcome.new - cbind(outcome, compkey, armkey) invalid.ids - outcome.new[outcome.new$compkey == outcome.new$armkey, c(Assessment_record_ID)] Error in Ops.factor(outcome.new$compkey, outcome.new$armkey) : level sets of factors are different Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-6692tel:%2B91-40-6692 and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). [[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] prevalence of R in publications and institutions
On Fri, Aug 17, 2012 at 6:46 AM, Travis Perry travis.pe...@furman.edu wrote: Dr. Bates, Our department is considering replacing existing statistical software packages in our curriculum with R, at my request. To better inform this decision we are interested to know the prevalence of R in the published literature and its use across academic and research institutions. I have so far been unable to find satisfactory information on the subject. Any information you could provide would be much appreciated. Thank you in advance for your time and consideration. best, -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 Because R is an Open Source system which is freely distributed and may be freely redistributed there is no way of keeping track of the downloads and its use in academic and research institutions. Searching for R statistics at a book site such as amazon.com or barnesandnoble.com should produce enough hits to convince your colleagues of an active development community. On scholar.google.com the system itself has been cited 3782 times and the initial paper on the system by Ihaka and Gentleman has been cited over 6000 times. Others on the R-help list may be able to give more information regarding the use of R in the biological sciences. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Remove several numbers from a sequence
Can anyone tell me how to remove several numbers for a sequence. For example: xx- c(1,5,7,10) yy-seq(1,10,1) how do I get take xx away from yy to get the new sequence 2,3,4,6,8,9 Many thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Remove-several-numbers-from-a-sequence-tp4640630.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] RGDAL OGRwrite question
I have a quick question: It appears that in rgdal v0.7-12 (R version
2.15.1, OSX 10.6.8) writeOGR will not write a shapefile the the
current directory. Is this correct? An earlier version of rgdal must
have allowed this because I have a older script that used to work, but
doesn't now.
So, as an example, here is what I get today:
shape = readOGR('.', layer='S20_G75_V00_HAASHP10_R00')
OGR data source with driver: ESRI Shapefile
Source: ., layer: S20_G75_V00_HAASHP10_R00
with 169 features and 23 fields
Feature type: wkbPolygon with 2 dimensions
writeOGR(shape, '.', layer='temp', driver='ESRI Shapefile', verbose=TRUE)
Error in writeOGR(shape, ., layer = temp, driver = ESRI Shapefile) :
Creation of output file failed
writeOGR(shape, '/tmp', layer='temp', driver='ESRI Shapefile',verbose=TRUE)
$object_type
[1] SpatialPolygonsDataFrame
$output_dsn
[1] /tmp
$output_layer
[1] temp
$output_diver
[1] ESRI Shapefile
$output_n
[1] 169
$output_nfields
[1] 23
$output_fields
[1] ID ANID F_AREA Avg_z Manning
[6] IniWL IniSal DispCoeff HydRad veg1_DW
[11] veg2_IWveg3_SWveg4_DCveg5_ICveg6_SC
[16] veg7_Marsh veg8_Swamp Rain_StID WetlandOpenwater
[21] iniBed_m maxH_m BoxID
$output_fclasses
[1] 0 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 4
$dataset_options
NULL
$layer_options
NULL
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room 141
Lafayette, LA 70504
Mailing address : UL Lafayette
Department of Biology
P.O.Box 42451
Lafayette, LA 70504-2451
Phone : 337 482 5304
Fax : 337 482 5834
email : smd3...@louisiana.edu
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Re: [R] Error: level sets of factors are different?
Hello, The message is not about lengths, it's about sets. It means that the two factors, compkey and armkey don't have the same levels, which you can see with levels(compkey) levels(armkey) and test for equality. Also, your post's prologue doesn't have a direct relation with the error, you could have skipped the lines up to, including, sink(). It's much better to provide an actual data example: dput( head(outcome, 50) ) # paste the output of this in a post. Hope this helps, Rui Barradas Em 17-08-2012 14:01, Sri krishna Devarayalu Balanagu escreveu: Why the error is coming? even though the length of outcome.new$compkey and outcome.new$armkey were exactly same. Can anyone help? setwd(D:/AZ) library(RODBC) cdb_cnct - odbcConnectExcel(AZIF_DC_GVK_NSCLC_MSALL_287papers_02072012_141450_v1_4.xls) outcomes - sqlFetch(cdb_cnct, Outcomes_info) odbcClose(cdb_cnct) rm(cdb_cnct) sink(Dependency checks.log) outcomes[(outcomes$Comparator != ), ] - outcome compkey - paste(outcome$Comparator, outcome$Comparator_Subarm, sep='_') armkey - paste(outcome$Arm_ID, outcome$SubArm_ID, sep='_') outcome.new - cbind(outcome, compkey, armkey) invalid.ids - outcome.new[outcome.new$compkey == outcome.new$armkey, c(Assessment_record_ID)] Error in Ops.factor(outcome.new$compkey, outcome.new$armkey) : level sets of factors are different Notice: The information contained in this electronic mail message is intended only for the use of the designated recipient. This message is privileged and confidential. and the property of GVK BIO or its affiliates and subsidiaries. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this message in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by telephone +91-40-6692tel:%2B91-40-6692 and destroy any and all copies of this message in your possession (whether hard copies or electronically stored copies). [[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] Plot multiple variables: label points
I know about the text function, it works well if I plot just 2 variables - I give the x and the y coordinates, but I doesn't work if i try to do this in this plot whith the multiple variables: *time1 plot plot plot time2 plot plot plot time3* so what would the solution? variable[,2:4] are the columns time1, time2 and time3 text(variable[,2:4],variable$group) doesn't work - give me an error - unable to convert object to double. What should be the x- and the y-values if every plot has its own x-y-scale? text(variable$time1, variable$time2, variable$group) just doesn't appear on the plot? -- View this message in context: http://r.789695.n4.nabble.com/Plot-multiple-variables-label-points-tp4640611p4640626.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] Plot multiple variables: label points
The provided solution is: panel.text - function(x, y, text, ...) text (x, y, labels = text) pairs(variable[,2:4], pch=19, text = variable$group, lower.panel = panel.text, upper.panel = panel.text) -- View this message in context: http://r.789695.n4.nabble.com/Plot-multiple-variables-label-points-tp4640611p4640629.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] set working directory to current source directory
Subject: Re: [R] set working directory to current source directory
A windows-centric work-round (assuming .Rdata files are 'associated' with the
right R binary n installation) is to save an empty environment in the relevant
project directory with the source file you would normally run. Starting R by
clicking on .Rdata file opens R in the right directory to start with. Using
relative paths in scripts thereafter then keeps things within the project work
area. Starting the first script with rm(list=ls()) guards against inadvertent
inclusion of old data (and even apparently 'empty' environments aren't
necessarily empty, so I clean up regardless if I start a session that way).
S Ellison
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] prevalence of R in publications and institutions
On 08/17/2012 09:25 AM, Douglas Bates wrote: On Fri, Aug 17, 2012 at 6:46 AM, Travis Perry travis.pe...@furman.edu wrote: Dr. Bates, Our department is considering replacing existing statistical software packages in our curriculum with R, at my request. To better inform this decision we are interested to know the prevalence of R in the published literature and its use across academic and research institutions. I have so far been unable to find satisfactory information on the subject. Any information you could provide would be much appreciated. Thank you in advance for your time and consideration. best, -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 Because R is an Open Source system which is freely distributed and may be freely redistributed there is no way of keeping track of the downloads and its use in academic and research institutions. Searching for R statistics at a book site such as amazon.com or barnesandnoble.com should produce enough hits to convince your colleagues of an active development community. On scholar.google.com the system itself has been cited 3782 times and the initial paper on the system by Ihaka and Gentleman has been cited over 6000 times. Others on the R-help list may be able to give more information regarding the use of R in the biological sciences. The Bioconductor annual report includes attempts to quantify scholarly citations http://bioconductor.org/about/annual-reports/ The July 2012 report section 1.4 indicates 4115 Google Scholar citations of Gentleman et al., 2004, which introduced the project. There were at least 321 PubMed citations with the term 'Bioconductor' in 2011. A fun game is to open your favourite high-profile science journal and play spot-the-R-or-Bioconductor figure or analysis; this is not a challenging game. 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. -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Remove several numbers from a sequence
Take a look at ?setdiff Michael On Aug 17, 2012, at 12:18 PM, penguins cat...@bas.ac.uk wrote: Can anyone tell me how to remove several numbers for a sequence. For example: xx- c(1,5,7,10) yy-seq(1,10,1) how do I get take xx away from yy to get the new sequence 2,3,4,6,8,9 Many thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Remove-several-numbers-from-a-sequence-tp4640630.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 multiple variables: label points
When you call plot with more than two columns, uses the pairs() function. That means you have to write a panel function. Here are a couple of relatively simple examples: pairs(variable[,2:4], panel=function(x, y, ...) text(x, y, variable$group)) pairs(variable[,2:4], panel=function(x, y, ...) points(x, y, pch=as.numeric(variable$group))) The first one plots the group instead of a point and the second one plots a symbol for each group. -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Bert Gunter Sent: Friday, August 17, 2012 9:18 AM To: cm256 Cc: r-help@r-project.org Subject: Re: [R] Plot multiple variables: label points ?text Have you read the Introduction to R tutorial. If not, do so before further posting. If so, re-read section 12.2. -- Bert On Fri, Aug 17, 2012 at 6:33 AM, cm256 d-...@gmx.at wrote: Hello, I have a data.frame with 10-15 entries which looks like this: group time1 time2 time3 1 F18 4394.500 21043.50 14949.00 2 F25 4678.000 23727.65 15683.12 3 F30 4909.775 23487.60 16724.40 I plot this with: plot(variable[,2:4]) so that a plot with 3 rows and 3 lines for time1, time2 and time3 appears. Is it somehow possible to label the data points with the values stored in group (F18, F25...)? -- View this message in context: http://r.789695.n4.nabble.com/Plot- multiple-variables-label-points-tp4640611.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. -- 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Remove several numbers from a sequence
HI, Try this: yy[is.na(match(yy,xx))] #[1] 2 3 4 6 8 9 A.K. - Original Message - From: penguins cat...@bas.ac.uk To: r-help@r-project.org Cc: Sent: Friday, August 17, 2012 12:18 PM Subject: [R] Remove several numbers from a sequence Can anyone tell me how to remove several numbers for a sequence. For example: xx- c(1,5,7,10) yy-seq(1,10,1) how do I get take xx away from yy to get the new sequence 2,3,4,6,8,9 Many thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Remove-several-numbers-from-a-sequence-tp4640630.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] Remove several numbers from a sequence
On 17-08-2012, at 18:18, penguins wrote: Can anyone tell me how to remove several numbers for a sequence. For example: xx- c(1,5,7,10) yy-seq(1,10,1) how do I get take xx away from yy to get the new sequence 2,3,4,6,8,9 You can also do this yy[!(yy %in% xx)] Berend __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] sample from a joint distribution of discrete continuous variables (survival analysis)
Dear All, My question is from the simulation of survival time with censoring indicator. Suppose I have a person with: 1. exponential life time, h(t) = lambda* exp(- lambda* t), some known lambda0. 2. a pre-determined event time, constant T; 3. a censoring indicator, delta=0 if the observed life time is greater than T, =1 other wise. I would like to sample (t, delta). According to some textbooks in this field, the joint distribution f (t, delta) = h(t) ^ delta * S(t) ^ (1 - delta) = lambda ^ delta * S(t) , where S(t) = integrated h(s) from 0 to t. = lambda^ delta * exp (- lambda*t ) What I did earlier was to sample t from the h(t), compare it with T and obtain delta, But I am not confidient with this approach. Could anyone give an example or idea, please? And in general, how do solve this kind of problem? Inversing the uniform random variable is only for continuous case? Thank you for your time. Best wishes, Jie [[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] Get the filename from the given path
Q. Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? A. x - substr(FPath,13,nchar(FPath)) should give you the desired output. But this is much like saying x - MyFile.txt will give you the desired output - where did the 13 come from? Use basename() for a general solution. basename(FPath) [1] MyFile.txt dirname(FPath) gives you the directory that FPath is in in. (To other responders, those who don't know that all caps means shouting probably don't know that the answer '?basename' means to type that into R to look at the help file for the basename function.) 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 Rantony Sent: Friday, August 17, 2012 4:56 AM To: r-help@r-project.org Subject: Re: [R] Get the filename from the given path Thanks pramod. From: Pramod [via R] [mailto:ml-node+s789695n4640600...@n4.nabble.com] Sent: Friday, August 17, 2012 5:24 PM To: Akkara, Antony (GE Energy, Non-GE) Subject: Re: Get the filename from the given path x - substr(FPath,13,nchar(FPath)) should give you the desired output. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp464 0578p4640600.html To unsubscribe from Get the filename from the given path, click here http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscrib e_by_codenode=4640578code=YW50b255LmFra2FyYUBnZS5jb218NDY0MDU3OHwx NTUx OTQzMDI5 . NAML http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_view erid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.Bas icNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.tem plate.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml -instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemai l.naml -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from- the-given-path-tp4640578p4640601.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] dimnames in an array(I'll be grateful if this message will be passed to all list users)
On Aug 17, 2012, at 9:25 AM, aleksandr shfets a_shf...@mail.ru wrote: Michael, Thank you for suggestions; it seems to me that there's a fundamental lacuna with respect to names of a three dimensional array: A lacuna in the English language, not in R: though perhaps Prof Ripley's employer's dictionary's editors could help us out ;-) [that might be the closest I've ever gotten to chained pointers in a natural language] that is, rownames fits dimension 1, colnames fits another dimension(that is, 3, if I read it correctly), but there is no specific name for the third dimension. I've tried setnames thinking that this would be appropriate for naming the sets, but there is no such R function. On the other hand you're right, the suggestion dimnames(data11a)[[2]]=c(V,R) doesn't ameliorate the analysis: while now dimnames(data11a)[[2]] comes out as [2] returning to the original analysis the same error comes up, that is, that the length of dimnames[2] doesn't agree with thee. I don't believe I made any prescriptions about length(dimnames[2]) so I have no idea what you mean here about it not agreeing with me. Also, there's almost no chance that's valid syntax: it should throw a 'closure not subsettable' error unless you over-wrote the name of a very important function (which you should not do). And I believe I told you that you want double brackets here. 'array extent' -- that is, even though the boxcar contents are two in number, it evaluates the analysis on the basis of the dimnames(data11a)[2] value. No! Double brackets. I'm using colloc infer (available under R 2.14) and trying to do the FHN(FitzHugh Nagumo) analysis in section 9.1 of the manual; it's very complex work, but I doubt the program is in error. I'm travelling currently so I can't track this down (no wifi) but I'll try later. In the meanwhile, see Bill Dunlap's suggestions. It seems to me in any case that, if R demands that the length of 'dimnames[2] must be equal to the array extent, then there must be a way to make the length of the names equal to the extent of the array, am I right? Again -- your code (dimnames[2]) looks like nonsense -- I think you've overwritten a function that you shouldn't have. Otherwise R would be inconsistent with itself, like Nomad on Startrek, and I've never seen a case where it was thus. Really? Never thought about the S3 naming conventions then This is again why I ask if others with extensive experience with dimnames of an array have seen anything similar. Certainly someone might know what is the significance of the dimnames of the array, how much can the length of them be altered for use generally? Dimnames must have lengths which correspond to the dimensions of the underlying array -- that is dim(a) == sapply(dimnames(a) length) Nothing else really makes sense. The only way to change the lengths of the dimnames is to reshape the array. Michael regards, A Thu, 16 Aug 2012 00:00:35 -0400 Ð¾Ñ R. Michael Weylandt michael.weyla...@gmail.com: On Wed, Aug 15, 2012 at 3:57 AM, aleksandr shfets a_shf...@mail.ru wrote: Hi Michael, Thanks for help on double brackets: I wasn't aware of this use of them. I went back to readjust my array so the dimnames(data11a)[[2]] would have two elements, and remade the array to include the new dimnames: dimnames(data11a)[[2]]=c(V,R) so that inside the second car of the train would be two items? Yes. There seems to be no way to define dimnames(data11a)[2] to be two elements rather than one[as you say we have no way to combine the elements of the train except using the train]. You could do this: dimnames(data11a)[2] - list(c(V,R)) but I'm not sure that's any clearer. To keep the metaphor rolling (get it!), list() puts your stuff in a boxcar so now you can put it directly on the train. So having tried to do what I can to make the middle element of the list to two rather than one, I rerun the analysis with the same result. if I read the thing right, regardless of how I define the inside of the boxcar, the analysis that I referred to res11a = inneropt(coefs, times=times, data=data11a, lik=lik, proc=proc, pars=spars, in.meth='nlminb', control.in=control.out) Where is this inneropt function from? It could be an error in that. If it's from a package, give me the name and I'll take a look at it and you can also contact the maintainer: get contact info using the maintainer() function. Also, some of the advice here will probably be helpful in seeking follow-up: http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example Cheers, Michael still won't look at the 'contents' of the car, but gives the same message: Error in `colnames-`(`*tmp*`, value = c(V, R)) : length of 'dimnames' [2] not equal to array extent I've tried a couple of other things like, after
Re: [R] Error: level sets of factors are different?
The cbind method to data.frame is just a wrapper for data.frame(...). So character columns are converted to factors. dat - cbind(data.frame(x = 1:3), a = c(a, b, c), b = c(a, a, c)) str(dat) ## 'data.frame': 3 obs. of 3 variables: ## $ x: int 1 2 3 ## $ a: Factor w/ 3 levels a,b,c: 1 2 3 ## $ b: Factor w/ 2 levels a,c: 1 1 2 dat$a == dat$b ## Error in Ops.factor(dat$a, dat$b) : level sets of factors are different as.character(dat$a) == as.character(dat$b) ## [1] TRUE FALSE TRUE dat - cbind(data.frame(x = 1:3), a = c(a, b, c), b = c(a, a, c), stringsAsFactors = FALSE) str(dat) ## 'data.frame': 3 obs. of 3 variables: ## $ x: int 1 2 3 ## $ a: chr a b c ## $ b: chr a a c dat$a == dat$b ## [1] TRUE FALSE TRUE -- Noia Raindrops noia.raindr...@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] Remove several numbers from a sequence
yy[!yy%in%xx] Clint BowmanINTERNET: cl...@ecy.wa.gov Air Quality Modeler INTERNET: cl...@math.utah.edu Department of Ecology VOICE: (360) 407-6815 PO Box 47600FAX:(360) 407-7534 Olympia, WA 98504-7600 USPS: PO Box 47600, Olympia, WA 98504-7600 Parcels:300 Desmond Drive, Lacey, WA 98503-1274 On Fri, 17 Aug 2012, penguins wrote: Can anyone tell me how to remove several numbers for a sequence. For example: xx- c(1,5,7,10) yy-seq(1,10,1) how do I get take xx away from yy to get the new sequence 2,3,4,6,8,9 Many thanks in advance -- View this message in context: http://r.789695.n4.nabble.com/Remove-several-numbers-from-a-sequence-tp4640630.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] Unequal splits from a column
Here's a slightly different approach without regular expressions: dat1-data.frame(slope=c(slope (60/25/15),slope (90/10), slope (40/35/15/10),slope (40/25/25/10) )) tmp - strsplit(as.character(dat1$slope), split=[/()]) tmp2 - sapply(tmp, function(x) as.numeric(x[-1])) maxlen - max(sapply(tmp2, length)) datnew - data.frame(t(sapply(tmp2, function(x) c(x, rep(0, maxlen-length(x)) datnew X1 X2 X3 X4 1 60 25 15 0 2 90 10 0 0 3 40 35 15 10 4 40 25 25 10 -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of arun Sent: Friday, August 17, 2012 6:56 AM To: Sapana Lohani Cc: R help Subject: Re: [R] Unequal splits from a column HI, Try this: dat1-data.frame(slope=c(slope (60/25/15),slope (90/10),slope (40/35/15/10),slope (40/25/25/10) )) dat1$slope-gsub(slope\\s+.*(\\(.*\\)),\\1,dat1$slope) dat1$slope-gsub(\\((.*)\\),\\1,dat1$slope) dat2-strsplit(dat1$slope,/) dat2[[1]][4]-0 dat2[[2]][3:4]-0 data.frame(do.call(rbind,dat2)) # X1 X2 X3 X4 #1 60 25 15 0 #2 90 10 0 0 #3 40 35 15 10 #4 40 25 25 10 - Original Message - From: Sapana Lohani lohani.sap...@ymail.com To: r-help@r-project.org r-help@r-project.org Cc: Sent: Friday, August 17, 2012 1:05 AM Subject: [R] Unequal splits from a column Hi I am new to R so am struggling with the commands here I have one column in a table that looks like slope (60/25/15) slope (90/10) slope (40/35/15/10) slope (40/25/25/10) I want to have 4 columns with just the number inside the parenthesis. when there is no number that cell can have 0. I want the output like this 60 25 15 0 90 10 0 0 40 35 15 10 40 25 25 10 Can somebody help me?? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] mixed model in r
Dear all, I am really confused with the syntax for mixed model using lmer in lme4 library. My model is Value = Sample + Run (nested with Sample ) Here sample is a fixed effect and Run is a random effect nested with sample. Can anyone give some hint on the correct syntex for this model. Thanks very much in advance. Hannah [[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] Opinion: Why I find factors convenient to use
Folks: Over the years, many people -- including some who I would consider real expeRts -- have criticized factors and advocated the use (sometimes exclusively) of character vectors instead. I would just like to point out that, for me, factors provide one feature that I find to be very convenient: ordering of levels. ** As an example, suppose one has a character vector of labels small, medium, and large. Then most R functions (e.g. tapply()) will display results involving this vector in alphabetical order, which I think most would view as undesirable. By converting to a factor with levels in the logical order, displays will automatically be logical. For example: x - sample(c(small,medium,large),12,rep=TRUE) table(x) x large medium small 2 3 7 y - factor(x,lev=c(small,medium,large)) ##ordered() also would do, but is not necessary for this table(y) y small medium large 7 3 2 Naturally, this is just my opinion, and I understand why lots of smart people find factors irritating (at least!). So contrary opinions cheerily welcomed. But perhaps these comments might be helpful to those who have been bitten by factors or just wonder what all the fuss is about. ** Another advantage is reduced storage space, I believe. Please correct if wrong. Cheers, Bert -- 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] Opinion: Why I find factors convenient to use
I second to Bert's opinion, factors can be confusing, but they have quite nice features which can not be easily mimicked by plain character vectors. I find extremelly usefull possibility of manipulating its levels. fac-factor(sample(letters[1:5], 20, replace=TRUE)) fac [1] e e d d e e c e a e a e b b d e c c d b Levels: a b c d e levels(fac)[2:4]- new.level fac [1] e e new.level new.level e e new.level [8] e a e a e new.level new.level [15] new.level e new.level new.level new.level new.level Levels: a new.level e Regards Petr Odesílate: r-help-boun...@r-project.org [r-help-boun...@r-project.org] za uživatele Bert Gunter [gunter.ber...@gene.com] Odesláno: 17. srpna 2012 19:32 To: r-help@r-project.org Předmět: [R] Opinion: Why I find factors convenient to use Folks: Over the years, many people -- including some who I would consider real expeRts -- have criticized factors and advocated the use (sometimes exclusively) of character vectors instead. I would just like to point out that, for me, factors provide one feature that I find to be very convenient: ordering of levels. ** As an example, suppose one has a character vector of labels small, medium, and large. Then most R functions (e.g. tapply()) will display results involving this vector in alphabetical order, which I think most would view as undesirable. By converting to a factor with levels in the logical order, displays will automatically be logical. For example: x - sample(c(small,medium,large),12,rep=TRUE) table(x) x large medium small 2 3 7 y - factor(x,lev=c(small,medium,large)) ##ordered() also would do, but is not necessary for this table(y) y small medium large 7 3 2 Naturally, this is just my opinion, and I understand why lots of smart people find factors irritating (at least!). So contrary opinions cheerily welcomed. But perhaps these comments might be helpful to those who have been bitten by factors or just wonder what all the fuss is about. ** Another advantage is reduced storage space, I believe. Please correct if wrong. Cheers, Bert -- 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Opinion: Why I find factors convenient to use
I don't know if my recent post on this prompted your post, but I don't see much to argue with in your discussion. I find factors to be useful for managing display and some kinds of analysis. However, I find them mostly a handicap when importing, merging, and handling data QC. Therefore I delay conversion until late in the game... but usually I do eventually convert in most cases. --- 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. Bert Gunter gunter.ber...@gene.com wrote: Folks: Over the years, many people -- including some who I would consider real expeRts -- have criticized factors and advocated the use (sometimes exclusively) of character vectors instead. I would just like to point out that, for me, factors provide one feature that I find to be very convenient: ordering of levels. ** As an example, suppose one has a character vector of labels small, medium, and large. Then most R functions (e.g. tapply()) will display results involving this vector in alphabetical order, which I think most would view as undesirable. By converting to a factor with levels in the logical order, displays will automatically be logical. For example: x - sample(c(small,medium,large),12,rep=TRUE) table(x) x large medium small 2 3 7 y - factor(x,lev=c(small,medium,large)) ##ordered() also would do, but is not necessary for this table(y) y small medium large 7 3 2 Naturally, this is just my opinion, and I understand why lots of smart people find factors irritating (at least!). So contrary opinions cheerily welcomed. But perhaps these comments might be helpful to those who have been bitten by factors or just wonder what all the fuss is about. ** Another advantage is reduced storage space, I believe. Please correct if wrong. Cheers, Bert -- 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. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Opinion: Why I find factors convenient to use
Hi, On Fri, Aug 17, 2012 at 1:58 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I don't know if my recent post on this prompted your post, but I don't see much to argue with in your discussion. I find factors to be useful for managing display and some kinds of analysis. However, I find them mostly a handicap when importing, merging, and handling data QC. Therefore I delay conversion until late in the game... but usually I do eventually convert in most cases. Agreed here -- I actually haven't been tuned into any such recent conversation (if there was one), but if I were a gambling man, I'd bet that the majority of the problems people have with factors can probably be boiled down to the fact that the default value for stringsAsFactors is TRUE. I like factors -- that said, I am annoyed by them at times, but I still like them. Also, Bert mentioned that he thinks they save space over characters -- I believe that this is no longer true, but I'm not certain. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Opinion: Why I find factors convenient to use
Steve, et. al: Yes, if object.size() is to be believed, you're right: x -sample(c(small,medium,large),1e4,rep=TRUE) y - factor(x) object.size(x) 40120 bytes object.size(y) 40336 bytes I stand (happily) corrected. -- Bert On Fri, Aug 17, 2012 at 11:09 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, On Fri, Aug 17, 2012 at 1:58 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I don't know if my recent post on this prompted your post, but I don't see much to argue with in your discussion. I find factors to be useful for managing display and some kinds of analysis. However, I find them mostly a handicap when importing, merging, and handling data QC. Therefore I delay conversion until late in the game... but usually I do eventually convert in most cases. Agreed here -- I actually haven't been tuned into any such recent conversation (if there was one), but if I were a gambling man, I'd bet that the majority of the problems people have with factors can probably be boiled down to the fact that the default value for stringsAsFactors is TRUE. I like factors -- that said, I am annoyed by them at times, but I still like them. Also, Bert mentioned that he thinks they save space over characters -- I believe that this is no longer true, but I'm not certain. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact -- 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.
[R] spatial auto-correlation structure in nlme
Dear R users, I'm estimating a mixed effects model in which the spatial correlation is controlled for by the corGaus structure. I'm wondering if there is a document or paper that explains how the spatial correlation structure (such as corExp or corGaus) works. Let me use the example and data posted on UCLA's R FAQ webpage to explain my problems. The link for the webpage is: http://www.ats.ucla.edu/stat/r/faq/spatial_regression.htm install.packages(nlme) library(nlme) spdata - read.table(http://www.ats.ucla.edu/stat/R/faq/thick.csv;, header = T, sep = ,) dummy - rep(1, 75) spdata - cbind(spdata, dummy) ### estimate the null model ### soil.model - lme(fixed = thick ~ soil, data = spdata, random = ~ 1 | dummy, method = ML) summary(soil.model) plot(Variogram(soil.model,form=~north+east)) ### updated the model by the spatial correlation structure soil.gaus - update(soil.model, correlation=corGaus(1,form=~north+east)) summary(soil.gaus) plot(Variogram(soil.gaus,form=~north+east)) My questions are: 1) Is there a way that I can tell, to what extent the spatial correlation has been controlled for by the model, besides the improvements of AIC, BIC, and Loglik? 2) where can I find the formulas for the corExp or corGaus? Thanks! Gary [[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] Opinion: Why I find factors convenient to use
Hello, No, factors may use less memory. System dependent? x -sample(c(small,medium,large),1e4,rep=TRUE) y - factor(x) object.size(x) 80184 bytes object.size(y) 40576 bytes sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Portuguese_Portugal.1252 LC_CTYPE=Portuguese_Portugal.1252 [3] LC_MONETARY=Portuguese_Portugal.1252 LC_NUMERIC=C [5] LC_TIME=Portuguese_Portugal.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rcapture_1.2-0 xts_0.8-0 zoo_1.7-7 loaded via a namespace (and not attached): [1] chron_2.3-39 fortunes_1.4-2 grid_2.15.1lattice_0.20-6 tools_2.15.1 And I agree with what Steve said, stringsAsFactors = FALSE saves hours of debuging time. Rui Barradas Em 17-08-2012 19:19, Bert Gunter escreveu: Steve, et. al: Yes, if object.size() is to be believed, you're right: x -sample(c(small,medium,large),1e4,rep=TRUE) y - factor(x) object.size(x) 40120 bytes object.size(y) 40336 bytes I stand (happily) corrected. -- Bert On Fri, Aug 17, 2012 at 11:09 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, On Fri, Aug 17, 2012 at 1:58 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: I don't know if my recent post on this prompted your post, but I don't see much to argue with in your discussion. I find factors to be useful for managing display and some kinds of analysis. However, I find them mostly a handicap when importing, merging, and handling data QC. Therefore I delay conversion until late in the game... but usually I do eventually convert in most cases. Agreed here -- I actually haven't been tuned into any such recent conversation (if there was one), but if I were a gambling man, I'd bet that the majority of the problems people have with factors can probably be boiled down to the fact that the default value for stringsAsFactors is TRUE. I like factors -- that said, I am annoyed by them at times, but I still like them. Also, Bert mentioned that he thinks they save space over characters -- I believe that this is no longer true, but I'm not certain. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Opinion: Why I find factors convenient to use
On Fri, Aug 17, 2012 at 11:34 AM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, No, factors may use less memory. System dependent? I think it's a 32-bit vs. 64-bit distinction - I get Rui's results on 64-bit Windows and Linux installation, but Bert's result on a 32-bit Linux machine. Peter x -sample(c(small,medium,large),1e4,rep=TRUE) y - factor(x) object.size(x) 80184 bytes object.size(y) 40576 bytes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RGDAL OGRwrite question
Are the output files already there?
In that case, try overwrite_layer=TRUE
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 8/17/12 9:28 AM, Scott Duke-Sylvester scottdukesylves...@gmail.com
wrote:
I have a quick question: It appears that in rgdal v0.7-12 (R version
2.15.1, OSX 10.6.8) writeOGR will not write a shapefile the the
current directory. Is this correct? An earlier version of rgdal must
have allowed this because I have a older script that used to work, but
doesn't now.
So, as an example, here is what I get today:
shape = readOGR('.', layer='S20_G75_V00_HAASHP10_R00')
OGR data source with driver: ESRI Shapefile
Source: ., layer: S20_G75_V00_HAASHP10_R00
with 169 features and 23 fields
Feature type: wkbPolygon with 2 dimensions
writeOGR(shape, '.', layer='temp', driver='ESRI Shapefile',
verbose=TRUE)
Error in writeOGR(shape, ., layer = temp, driver = ESRI Shapefile) :
Creation of output file failed
writeOGR(shape, '/tmp', layer='temp', driver='ESRI
Shapefile',verbose=TRUE)
$object_type
[1] SpatialPolygonsDataFrame
$output_dsn
[1] /tmp
$output_layer
[1] temp
$output_diver
[1] ESRI Shapefile
$output_n
[1] 169
$output_nfields
[1] 23
$output_fields
[1] ID ANID F_AREA Avg_z Manning
[6] IniWL IniSal DispCoeff HydRad veg1_DW
[11] veg2_IWveg3_SWveg4_DCveg5_ICveg6_SC
[16] veg7_Marsh veg8_Swamp Rain_StID WetlandOpenwater
[21] iniBed_m maxH_m BoxID
$output_fclasses
[1] 0 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 4
$dataset_options
NULL
$layer_options
NULL
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room 141
Lafayette, LA 70504
Mailing address : UL Lafayette
Department of Biology
P.O.Box 42451
Lafayette, LA 70504-2451
Phone : 337 482 5304
Fax : 337 482 5834
email : smd3...@louisiana.edu
This e-mail message (including any attachments) is for t...{{dropped:11}}
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Re: [R] RGDAL OGRwrite question
In the example I gave, the temp.shp, 'temp.bdf, etc ... do not
exist in the current working directory (.) before I call:
writeOGR(shape, '.', layer='temp', driver='ESRI Shapefile', verbose=TRUE)
I should have specified this. Also, the working directory permissions
are set to owner read/write/execute (unix: drwxr-xr-x).
On Fri, Aug 17, 2012 at 2:17 PM, MacQueen, Don macque...@llnl.gov wrote:
Are the output files already there?
In that case, try overwrite_layer=TRUE
-Don
--
Don MacQueen
Lawrence Livermore National Laboratory
7000 East Ave., L-627
Livermore, CA 94550
925-423-1062
On 8/17/12 9:28 AM, Scott Duke-Sylvester scottdukesylves...@gmail.com
wrote:
I have a quick question: It appears that in rgdal v0.7-12 (R version
2.15.1, OSX 10.6.8) writeOGR will not write a shapefile the the
current directory. Is this correct? An earlier version of rgdal must
have allowed this because I have a older script that used to work, but
doesn't now.
So, as an example, here is what I get today:
shape = readOGR('.', layer='S20_G75_V00_HAASHP10_R00')
OGR data source with driver: ESRI Shapefile
Source: ., layer: S20_G75_V00_HAASHP10_R00
with 169 features and 23 fields
Feature type: wkbPolygon with 2 dimensions
writeOGR(shape, '.', layer='temp', driver='ESRI Shapefile',
verbose=TRUE)
Error in writeOGR(shape, ., layer = temp, driver = ESRI Shapefile) :
Creation of output file failed
writeOGR(shape, '/tmp', layer='temp', driver='ESRI
Shapefile',verbose=TRUE)
$object_type
[1] SpatialPolygonsDataFrame
$output_dsn
[1] /tmp
$output_layer
[1] temp
$output_diver
[1] ESRI Shapefile
$output_n
[1] 169
$output_nfields
[1] 23
$output_fields
[1] ID ANID F_AREA Avg_z Manning
[6] IniWL IniSal DispCoeff HydRad veg1_DW
[11] veg2_IWveg3_SWveg4_DCveg5_ICveg6_SC
[16] veg7_Marsh veg8_Swamp Rain_StID WetlandOpenwater
[21] iniBed_m maxH_m BoxID
$output_fclasses
[1] 0 4 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 0 2 2 2 2 4
$dataset_options
NULL
$layer_options
NULL
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room 141
Lafayette, LA 70504
Mailing address : UL Lafayette
Department of Biology
P.O.Box 42451
Lafayette, LA 70504-2451
Phone : 337 482 5304
Fax : 337 482 5834
email : smd3...@louisiana.edu
This e-mail message (including any attachments) is for t...{{dropped:11}}
__
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.
--
Scott M. Duke-Sylvester
Assistant Professor
Department of Biology
Office : 300 E. St. Mary Blvd
Billeaud Hall, Room 141
Lafayette, LA 70504
Mailing address : UL Lafayette
Department of Biology
P.O.Box 42451
Lafayette, LA 70504-2451
Phone : 337 482 5304
Fax : 337 482 5834
email : smd3...@louisiana.edu
This e-mail message (including any attachments) is for the sole use of
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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Re: [R] Trouble compiling package on Windows (64 bit)
Uwe, I did give you the output from R CMD INSTALL (or at least, what I thought was the relevant part). Here is the output in toto: * installing to library 'C:/programming/r/revolutions/R-2.14.2/library' * installing *source* package 'KernGPLM' ... ** libs *** arch - i386 ERROR: compilation failed for package 'KernGPLM' * removing 'C:/programming/r/revolutions/R-2.14.2/library/KernGPLM' Any advice will be very useful. Thanks. - Original Message - From: Uwe Ligges lig...@statistik.tu-dortmund.de To: Fg Nu fgn...@yahoo.com Cc: r-help@r-project.org r-help@r-project.org Sent: Friday, August 17, 2012 4:45 AM Subject: Re: [R] Trouble compiling package on Windows (64 bit) On 17.08.2012 12:38, Fg Nu wrote: I am trying to compile the R package KernGPLM found here: http://www.marlenemueller.de/KernGPLM/KernGPLM_0.65.tar.gz since the binary available is for R 2.4. but the compilation ends with the error message: *** arch-i386 ERROR: compilation failed for the package 'KernGPLM' See the R Installation and Administration manual. It tells you how to set up an environment under Windows to be able to install the package from sources. We cannot say more without the actual output of R CMD INSTALL. Best, Uwe Ligges Here is my session info: R version 2.14.2 (2012-02-29) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods [7] base other attached packages: [1] Revobase_6.0.0 RevoMods_6.0.0 RevoScaleR_3.0-0 lattice_0.20-0 loaded via a namespace (and not attached): [1] codetools_0.2-8 foreach_1.4.0 grid_2.14.2 iterators_1.0.6 [5] tools_2.14.2 Is it possible to diagnose the problem from this information? 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] prevalence of R in publications and institutions
Thank you both for your time and assistance. On Fri, Aug 17, 2012 at 12:25 PM, Douglas Bates ba...@stat.wisc.edu wrote: ** ** On Fri, Aug 17, 2012 at 6:46 AM, Travis Perry travis.pe...@furman.edu wrote: Dr. Bates, Our department is considering replacing existing statistical software packages in our curriculum with R, at my request. To better inform this decision we are interested to know the prevalence of R in the published literature and its use across academic and research institutions. I have so far been unable to find satisfactory information on the subject. Any information you could provide would be much appreciated. Thank you in advance for your time and consideration. best, -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 Because R is an Open Source system which is freely distributed and may be freely redistributed there is no way of keeping track of the downloads and its use in academic and research institutions. Searching for R statistics at a book site such as amazon.com or barnesandnoble.com should produce enough hits to convince your colleagues of an active development community. On scholar.google.com the system itself has been cited 3782 times and the initial paper on the system by Ihaka and Gentleman has been cited over 6000 times. Others on the R-help list may be able to give more information regarding the use of R in the biological sciences. -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 [[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] Appending many different and separate Excel files using R
Dear all, Good day! I have a problem in reading Excel files in R and appending them to each other. Suppose we have several Excel files in a directory with headers and want to use R to append them in a single file with an additional variable in the final file indicating from which files the data come from. As I have many Excel files and their sizes are very big I should write a loop in R to do the work. I will be very happy if you guide and help me to write the codes. Thank you very much in advance. Kind regards, Amir Kasaeian Amir Kasaeian, PhD Student in Biostatistics, Dept. of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences (TUMS). P.B. : 14155-6446 Cell Phone: +98-912-2063511 E-mail: akasae...@razi.tums.ac.ir amir_kasae...@yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] prevalence of R in publications and institutions
From a blurb I wrote recently: Publishing on R has accelerated over the last few years. Chapman and Hall/CRC Press publish over 50 books on R and has recently issued a call for new submissions. Springer has a growing series called Use R! (38 volumes). Wiley has a series called Statistics Using R (28 volumes). -- David L Carlson Associate Professor of Anthropology Texas AM University College Station, TX 77843-4352 -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of Travis Perry Sent: Friday, August 17, 2012 3:14 PM To: Douglas Bates Cc: r-help Subject: Re: [R] prevalence of R in publications and institutions Thank you both for your time and assistance. On Fri, Aug 17, 2012 at 12:25 PM, Douglas Bates ba...@stat.wisc.edu wrote: ** ** On Fri, Aug 17, 2012 at 6:46 AM, Travis Perry travis.pe...@furman.edu wrote: Dr. Bates, Our department is considering replacing existing statistical software packages in our curriculum with R, at my request. To better inform this decision we are interested to know the prevalence of R in the published literature and its use across academic and research institutions. I have so far been unable to find satisfactory information on the subject. Any information you could provide would be much appreciated. Thank you in advance for your time and consideration. best, -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 Because R is an Open Source system which is freely distributed and may be freely redistributed there is no way of keeping track of the downloads and its use in academic and research institutions. Searching for R statistics at a book site such as amazon.com or barnesandnoble.com should produce enough hits to convince your colleagues of an active development community. On scholar.google.com the system itself has been cited 3782 times and the initial paper on the system by Ihaka and Gentleman has been cited over 6000 times. Others on the R-help list may be able to give more information regarding the use of R in the biological sciences. -- Travis Perry Associate Professor of Biology Department of Biology Furman University 3300 Poinsett Highway Greenville, SC 29613 Senior Research Associate Rhodes University Grahamstown, South Africa Cell (864)-561-4240 [[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] REPOST: Need help interpreting output from rcorrp.cens with Cox regression
I am reposting my message from April 8th because I never received a response to the original post: Dear R-listers, I am an MD and clinical epidemiologist developing a measure of comorbidity severity for patients with liver disease. Having developed my comorbidity score as the linear predictor from a Cox regression model I want to compare the discriminative ability of my comorbidity measure with the old comorbidity measure, Charlson's Comorbidity Index. I have nearly 10,000 deaths and 36 candidate comorbidities. I wish to compare the discrimination of the two comorbidity measures, i.e. I have two non-nested Cox models. I get the following output with rcorrp.cens(myscore.lp, charlson.lp, Surv(time, dead), method=1): x1 = My comorbidity score, x2 = Charlson [,1] Dxy-0.0605 S.D. 0.00648 x1 more concordant 0.4697 x2 more concordant 0.5302 n 1.369e+04 missing0 uncensored 9411 Relevant Pairs 1.587e+08 Uncertain 2.861e+07 C X1 0.395 C X2 0.401 Dxy X1 -0.21 Dxy X2 -0.198 I am aware that because a high hazard means short survival I must subtract C X1 and C X2 from 1, so my comorbidity score has marginally better discrimination than the Charlson score (C = 0.605 vs. 0.599). Question: Is it true that my score is more discriminative than the Charlson score in 53% of patient pairs? I have done the same analysis with 'method = 2', i.e. rcorrp.cens(myscore.lp, charlson.lp, Surv(time, dead), method=2): x1 = My comorbidity score, x2 = Charlson [,1] Dxy-0.006002 S.D. 0.001102 x1 more concordant 0.04018 x2 more concordant 0.04618 n 1.369e+04 missing0 uncensored 9411 Relevant Pairs 1.587e+08 Uncertain 2.861e+07 C X1 0.395 C X2 0.401 Dxy X1 -0.21 Dxy X2 -0.198 Question: How do I interpret the 'x1/x2 more concordant' numbers in a Cox regression setting? My guess: My comorbidity score concordant in 4.6% of pairs in which Charlson's score is not. And Charlson's score is concordant in 4.0% of pairs in which my comorbidity score is not. Thank you in advance for your insight and help. Best regards, Peter Jepsen Aarhus, Denmark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Appending many different and separate Excel files using R
On Aug 17, 2012, at 4:19 PM, Amir Kasaeian amir_kasae...@yahoo.com wrote: Dear all, Good day! I have a problem in reading Excel files in R and appending them to each other. Suppose we have several Excel files in a directory with headers and want to use R to append them in a single file with an additional variable in the final file indicating from which files the data come from. As I have many Excel files and their sizes are very big I should write a loop in R to do the work. I will be very happy if you guide and help me to write the codes. Thank you very much in advance. Given the overhead of most R/Excel interfaces, I think you might want to look into doing this within Excel only using some basic VBA. That said, do.call(rbind, lapply(dir(pattern = xls), function(n) read.xls(n))) should get you started. You can find read.xls in either the gdata or or xlsReadWrite packages. For more advanced control, look at the XLConnect package, which is, unfortunately, not currently available on OS X. Cheers, Michael Kind regards, Amir Kasaeian Amir Kasaeian, PhD Student in Biostatistics, Dept. of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences (TUMS). P.B. : 14155-6446 Cell Phone: +98-912-2063511 E-mail: akasae...@razi.tums.ac.ir ��� amir_kasae...@yahoo.com�� [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Opinion: Why I find factors convenient to use
Hello, Em 17-08-2012 20:27, Bert Gunter escreveu: ... so it may be just the way object.size() counts in the two cases, right? Or maybe the way character vectors and factors are coded. (64 bit Windows 7 or ubuntu 12.04) 80k for the character vector seems to be 8 * 1e4 for pointers plus room for the strings themselves, and 40k for the factor seems more like 32 bit ints * 1e4 in consecutive memory locations. I confess to being too lazy to go check the sources, but if this is the case then it's an other point to factors, they are indeed more efficient memory-wise. And 64 bit OSs are to become more and more used, processors aren't becoming worse. There is also the statistical side of it. Factors are the natural way of coding nominal or categorical variables. The small/medium/large example is a good one. Or seasons, we like to see Fall or Autumn after Spring and Summer, not before. (btw, does anyone know why M/F?) And this has nothing to do with the usefullness of charaters, I like persons' names to be names, alphabetic. I've also made a simple check, apparently, character vectors are kept as a vector of pointers and a vector of unique strings. If we change one of the strings, even for something smaller, occupying less bytes, object.size will report an increase in size. Try x[1] - a and see the new size of x. It's bigger and the number of pointers to strings is the same. For 32 and 64 bit Windows 7 and for 64 bit ubuntu 12.04, R was: R.version [...] version.string R version 2.15.1 (2012-06-22) nickname Roasted Marshmallows Rui Barradas -- Bert On Fri, Aug 17, 2012 at 11:42 AM, Peter Langfelder peter.langfel...@gmail.com wrote: On Fri, Aug 17, 2012 at 11:34 AM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, No, factors may use less memory. System dependent? I think it's a 32-bit vs. 64-bit distinction - I get Rui's results on 64-bit Windows and Linux installation, but Bert's result on a 32-bit Linux machine. Peter x -sample(c(small,medium,large),1e4,rep=TRUE) y - factor(x) object.size(x) 80184 bytes object.size(y) 40576 bytes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 utilizing 25% of CPU for Dual core i3 370M processor
Hello Everyone I have a dual-core Intel i3-370M processor and Windows 64 operating system. I have a 3GB RAM and my processor can support a maximum of 8GB RAM. I have virtual memory enabled on my computer. I am running a program in the 64 bit R which implements a MCMC on a large dataset and involves around 8 iterations. The processor estimates that it will take around 1000 minutes to complete running the program. However when I check the CPU usage it shows only 25% usage. I have read on threads that R runs on only 1 core - and thus was expecting a CPU usage of around 50%. It would be great if anyone can point out a way by which I can make the processor use 50% of the CPU which I believe would allow the program to be run quicker. Best Shantanu [[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] Get the filename from the given path
Yes, basename(filepath) assumes that filepath represents path to a file on the OS that R is running on. Hence, on Windows we get basename(dir\\path) [1] path basename(dir/path) [1] path because both / and \ are valid separators (and invalid in file names) Linux allows \ in a file name so we get basename(dir\\file) [1] dir\\file basename(dir/file) [1] file The same goes for dirname(): Windows dirname(c:/file) # c: is not a directory but c:/ is [1] c:/ Linux dirname(c:/file) [1] c: Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com -Original Message- From: arun [mailto:smartpink...@yahoo.com] Sent: Friday, August 17, 2012 1:20 PM To: William Dunlap Cc: Rantony; R help Subject: Re: [R] Get the filename from the given path Hi, I guess basename() output depends on the system. basename(getwd()) #[1] BehaviorStudy So, if I wanted to get the filename from the FPPath, I have to replace \\ to //. FPath - D:\\MyFolder\\MyFile.txt basename(FPath) #[1] D:\\MyFolder\\MyFile.txt FPath1-D://MyFolder//MyFile.txt basename(FPath1) #[1] MyFile.txt gsub(.*.*(.*),\\1,FPath) #[1] MyFile.txt gsub(.*\\//.*\\//(.*),\\1,FPath1) #[1] MyFile.txt A.K. - Original Message - From: William Dunlap wdun...@tibco.com To: Rantony antony.akk...@ge.com; r-help@r-project.org r-help@r-project.org Cc: Sent: Friday, August 17, 2012 11:41 AM Subject: Re: [R] Get the filename from the given path Q. Here i have a file path, for eg : - FPath - D:\\MyFolder\\MyFile.txt HOW IS POSSIBLE TO GET THE FILE NAME FROM THIS GIVEN PATH ? A. x - substr(FPath,13,nchar(FPath)) should give you the desired output. But this is much like saying x - MyFile.txt will give you the desired output - where did the 13 come from? Use basename() for a general solution. basename(FPath) [1] MyFile.txt dirname(FPath) gives you the directory that FPath is in in. (To other responders, those who don't know that all caps means shouting probably don't know that the answer '?basename' means to type that into R to look at the help file for the basename function.) 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 Rantony Sent: Friday, August 17, 2012 4:56 AM To: r-help@r-project.org Subject: Re: [R] Get the filename from the given path Thanks pramod. From: Pramod [via R] [mailto:ml-node+s789695n4640600...@n4.nabble.com] Sent: Friday, August 17, 2012 5:24 PM To: Akkara, Antony (GE Energy, Non-GE) Subject: Re: Get the filename from the given path x - substr(FPath,13,nchar(FPath)) should give you the desired output. If you reply to this email, your message will be added to the discussion below: http://r.789695.n4.nabble.com/Get-the-filename-from-the-given-path-tp464 0578p4640600.html To unsubscribe from Get the filename from the given path, click here http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscrib e_by_codenode=4640578code=YW50b255LmFra2FyYUBnZS5jb218NDY0MDU3OHwx NTUx OTQzMDI5 . NAML http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_view erid=instant_html%21nabble%3Aemail.namlbase=nabble.naml.namespaces.Bas icNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.tem plate.NodeNamespacebreadcrumbs=notify_subscribers%21nabble%3Aemail.naml -instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemai l.naml -- View this message in context: http://r.789695.n4.nabble.com/Get-the-filename-from- the-given-path-tp4640578p4640601.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R utilizing 25% of CPU for Dual core i3 370M processor
You probably have hyper threading so even though you only have two physical cores, there are 4 logical cores, hence 25%. Google can lead you to how to adjust this, if possible. Cheers, Josh On Fri, Aug 17, 2012 at 2:41 PM, Shantanu MULLICK b00295...@essec.edu wrote: Hello Everyone I have a dual-core Intel i3-370M processor and Windows 64 operating system. I have a 3GB RAM and my processor can support a maximum of 8GB RAM. I have virtual memory enabled on my computer. I am running a program in the 64 bit R which implements a MCMC on a large dataset and involves around 8 iterations. The processor estimates that it will take around 1000 minutes to complete running the program. However when I check the CPU usage it shows only 25% usage. I have read on threads that R runs on only 1 core - and thus was expecting a CPU usage of around 50%. It would be great if anyone can point out a way by which I can make the processor use 50% of the CPU which I believe would allow the program to be run quicker. Best Shantanu [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Making data in R available to Rcmdr
I'm an R newbie. I'm trying to use Rcmdr to make a 3-D scatterplot of data from a two-independent-variable regression and of the regression plane. The object dat in R contains the data: print(dat[1:20,]) y x1 x2 1 431.69 76.40 132.80 Rcmdr knows about dat. If I click Data, New data set, and enter the name dat, Rcmdr won't let me use that name. I get this message: Data set dat already exists. Overwrite data set? However, I don't know how to make dat the active data set in Rcmdr. Is that possible? Sorry if this is too basic. Can't find an answer in Getting Started With the R Commander or on this list. Todd -- View this message in context: http://r.789695.n4.nabble.com/Making-data-in-R-available-to-Rcmdr-tp4640672.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] Appending many different and separate Excel files using R
Hello, You need to provide us with a bit more information: Do all the files have the same structure, i.e., tables with the same columns? Are they xls, xlsx or csv files? Do their names share something in common such as a preffix or are they alone in the directory, or...? When you write in the final file does this mean that you want to output two files, one with the data and the other with the filenames? It would be nice if (a) the files were csv files, (b) if you answer to some or all of the rest, (c) anything that I might have forgotten and you find usefull. Rui Barradas Em 17-08-2012 22:19, Amir Kasaeian escreveu: Dear all, Good day! I have a problem in reading Excel files in R and appending them to each other. Suppose we have several Excel files in a directory with headers and want to use R to append them in a single file with an additional variable in the final file indicating from which files the data come from. As I have many Excel files and their sizes are very big I should write a loop in R to do the work. I will be very happy if you guide and help me to write the codes. Thank you very much in advance. Kind regards, Amir Kasaeian Amir Kasaeian, PhD Student in Biostatistics, Dept. of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences (TUMS). P.B. : 14155-6446 Cell Phone: +98-912-2063511 E-mail: akasae...@razi.tums.ac.ir amir_kasae...@yahoo.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Making data in R available to Rcmdr
Dear Todd, -Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of ToddE Sent: Friday, August 17, 2012 5:57 PM To: r-help@r-project.org Subject: [R] Making data in R available to Rcmdr I'm an R newbie. I'm trying to use Rcmdr to make a 3-D scatterplot of data from a two-independent-variable regression and of the regression plane. The object dat in R contains the data: print(dat[1:20,]) y x1 x2 1 431.69 76.40 132.80 Rcmdr knows about dat. If I click Data, New data set, and enter the name dat, Rcmdr won't let me use that name. I get this message: Data set dat already exists. Overwrite data set? However, I don't know how to make dat the active data set in Rcmdr. Is that possible? Data - New data set allows you to enter a new data set in the R data editor; it doesn't give you access to a data set that's currently in memory. Assuming that dat is a data frame (and that it really has more than just one line), you can access it either via Data - Active data set - Select active data set, or by clicking the No active dataset button in the Rcmdr toolbar. I hope this helps, John --- John Fox Senator McMaster Professor of Social Statistics Department of Sociology McMaster University Hamilton, Ontario, Canada Sorry if this is too basic. Can't find an answer in Getting Started With the R Commander or on this list. Todd -- View this message in context: http://r.789695.n4.nabble.com/Making-data- in-R-available-to-Rcmdr-tp4640672.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] Row means of matrix.
Hi all, I'm just having trouble getting row means of a matrix which contain zero. For example. m=matrix(c(1:4, c(0, 0, 0, 0), c(1, 0, 1, 1)), nc=4, byrow=TRUE) I want to be able to calculate means for non-zero elements for each row. ## what i have is this apply((m[apply(m != 0, MARGIN=1, any),]), 1, mean) ## which returns [1] 2.50 0.75 ### what i want to get returned is this [1] 2.50 *1 *meaning that the last row calculated the mean ignoring the zero. Anyone got any ideas? [[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] specific matrix element tranformation
Thanks David. I have actually 1 more question. How do I assign a name to the output created by this function? Cheers, B -- View this message in context: http://r.789695.n4.nabble.com/specific-matrix-element-tranformation-tp4640550p4640680.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] Row means of matrix.
On Aug 17, 2012, at 8:28 PM, Yingwei Lee wrote: m=matrix(c(1:4, c(0, 0, 0, 0), c(1, 0, 1, 1)), nc=4, byrow=TRUE) is.na(m) - m==0 rowMeans(m, na.rm=T) #[1] 2.5 NaN 1.0 -- David Winsemius, MD Alameda, CA, USA __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] no true negative data, need roc curve
This is not a typo error, in feature detection when it was not able to calculate 'tn' then they are using this formula and there are more papers (referred journal) which quote same formula. In the same manner i had also got the tp, fp and fn. Based on it can some one suggest me to plot the ROC curve for all the 6 data. http://r.789695.n4.nabble.com/file/n4640683/tpr2.jpg -- View this message in context: http://r.789695.n4.nabble.com/no-true-negative-data-need-roc-curve-tp4640474p4640683.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.
