[R] wavelets
I'm new to the topic of wavelets. When I tried to use the mra function in the wavelets package, the data is not getting compressed. eg. if the original data has 500 values , the output data also has the same. However in MATLAB, depending on the level of decompositon, the data gets compressed. How do I implement this in R? -- View this message in context: http://r.789695.n4.nabble.com/wavelets-tp3642973p3642973.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] superimposing different plot types in lattice panel.superpose
Hi:
Here's one way out, if I read your intention properly...
plot1 - xyplot(y ~ x, data = modelresults, groups = model, type = 'l',
xlim = c(0, 10), ylim = c(0.5, 3.5))
plot2 - xyplot(y ~ x, data = data, groups = model, type = 'p',
pch = 16, xlim = c(0, 10), ylim = c(0.5, 3.5))
plot1 + plot2
You might need latticeExtra to combine the plots (??); I had it loaded
with lattice when I did the plot.
HTH,
Dennis
On Sun, Jul 3, 2011 at 6:52 PM, genghis jcpa...@uw.edu wrote:
I would like to plot 3 best-fit models in a single panel of a lattice plot,
superimposed on 3 corresponding datasets in the same panel. My goal is to
show the models as lines of 3 different colors, and the data as points whose
colors correspond to the model colors. In essence, I have two levels of
grouping: 1) model vs. data, and 2) model number. Since there is only one
“groups” variable, I have tried to deal with the additional grouping level
by subsetting the data inside a custom panel function (basically a hack),
but something about the way parameters are passed in panel.superpose (I
think) is making it hard to show both points and lines.
My question is very similar to a previous post:
http://www.ask.com/web?q=r%20panel.superpose%20bwplot%20sim%20actualo=15527l=disprt=NISchn=retailgeo=USver=18
, but the questioner in that case was using bwplot, which automatically
makes a separate plot for every level of the categorical variable, so they
didn’t face the two-level grouping problem, and I have been unable to figure
out how to adapt their answer. Another approach I tried was to put my model
function inside of my custom panel function so that the analysis occurred
there, but I couldn’t get it to subset the x and y data appropriately.
In the toy problem below I want to plot each inverted V (“model”) as LINES,
with a single POINT (“data”) in the center of each inverted V, the same
color as the inverted V. The code runs, but I can’t seem to mix lines and
points. In my real problem (stable isotopes with ellipses superimposed on
data) there will be additional panels but I am creating only one panel here,
for simplicity.
#generate test model results
x-1:9
y-rep(c(1,3,1),3)
model-c(rep(a,3),rep(b,3),rep(c,3))
modelresults-data.frame(x,y,model)
#generate test data
x-c(2,5,8)
y-rep(1.5,3)
model-c(a,b,c)
data-data.frame(x,y,model)
#combine them into one data set
combined-make.groups(modelresults,data)
#custom panel function
panel.dualplot - function(...) {
panel.xyplot(x[which=modelresults],y[which=modelresults],...)
panel.points(x[which=data],y[which=data],...)
}
#main call to xyplot
xyplot(y ~ x, data=combined,
type = l,
panel = panel.superpose,
groups = model,
panel.groups = panel.dualplot,
)
I’d be very grateful for any suggestions.
Thanks!
John
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Re: [R] Poisson GLM with a logged dependent variable...just asking for trouble?
Dear Mark, I think you want glm(DV ~ log10(IV), family=poisson) Note that the poisson family uses the log-link by default. Hence you don't need to log-transform DV yourself. Best regards, Thierry ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens Mark Na Verzonden: vrijdag 1 juli 2011 23:10 Aan: r-help@r-project.org Onderwerp: [R] Poisson GLM with a logged dependent variable...just asking for trouble? Dear R-helpers, I'm using a GLM with poisson errors to model integer count data as a function of one non-integer covariate. The model formula is: log(DV) ~ glm(log(IV,10),family=poisson). I'm getting a warning because the logged DV is no longer an integer. I have three questions: 1) Can I ignore the warning, or is logging the DV (resulting in non-integers) a serious violation of the Poisson error structure? 2) If the answer to #1 is no, don't ignore it, it's serious then can I use a quasipoisson error structure instead (does not give the same warning) and if so are there any pitfalls to using the quasipoisson model? Are there any better alternatives for count data where the counts must be logged? Or, should I just abandon logging the DV? In that case, how could I compare the fit of a Poisson model (without logging the DV) to that of a GLM with normal errors (with a logged DV). AIC would not be valid because the DVs are different, right? 3) The quasipoisson model doesn't return an AIC value. Why, and is there anything I can do to calculate AIC manually, that would allow me to compare this model to other models? Many thanks in advance for your help! Cheers, Mark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] wavelets
Study the topic more carefully, I suppose. My understanding is that wavelets do not in themselves compress anything, but because they sort out the interesting data from the uninteresting data, it can be easy to toss the uninteresting data (lossy data compression). Perhaps you should understand better what your Matlab library is doing. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. user123 tyagi...@gmail.com wrote: I'm new to the topic of wavelets. When I tried to use the mra function in the wavelets package, the data is not getting compressed. eg. if the original data has 500 values , the output data also has the same. However in MATLAB, depending on the level of decompositon, the data gets compressed. How do I implement this in R? -- View this message in context: http://r.789695.n4.nabble.com/wavelets-tp3642973p3642973.html Sent from the R help mailing list archive at Nabble.com. _ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] RWinEdt problem
On 04.07.2011 06:56, Simon Knapp wrote: ... I just tried fiddling with the appearance settings, and when I uncheck Custom Colors under Document Tabs, the file names reappear, though I don't get the coloring I am used to (red for modified, green for unmodified). Right. That is fixed in RWinEdt 1.8-3 (i.e. customm coloring disabled) which has been uploaded to CRAN during the weekend. A Windows binary will be created shortly. Uwe Thanks again, Simon Knapp On Mon, Jul 4, 2011 at 2:48 PM, Simon Knappsleepingw...@gmail.com wrote: Hi R Helpers, I am a long time RWinEdt user and have just acquired a new laptop. I have installed RWinEdt and things are going smoothly except for one small glitch - file names are not appearing on the document tabs. When I use WinEdt (as opposed to RWinEdt), they are appearing. Can anyone offer any advice on this? Thanks in advance, Simon Knapp OS: windows7 Arch: 64 bit R version: 2.13.0 (2011-04-13) WinEdt version: 5.14 (build 20050701) [[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] Wrong environment when evaluating and expression?
Hi All, I have constructed two expressions (e1 e2). I can see that they are not identical, but I cannot figure out how they differ. ### dat - mtcars e1 - expression(with(data = dat, lm(mpg ~ hp))) e2 - as.expression(substitute(with(data = dat, lm(f)), list(f = mpg ~ hp))) str(e1) str(e2) all.equal(e1, e2) identical(e1, e2) # false eval(e1) eval(e2) The context is trying to use a list of formulae to generate several models from a multiply imputed dataset. The package I am using (mice) has methods for with() and that is how I can (easily) get the pooled results. Passing the formula directly does not work, so I was trying to generate the entire call and evaluate it as if I had typed it at the console, but I am missing something (probably rather silly). Thanks, Josh -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] [R-pkgs] rgdal 0.7-1 release
A new release of rgdal, a package providing bindings for the Geospatial Data Abstraction Library for reading and writing spatial data, has reached CRAN. This release changes the error handling mechanisms, and is more fully described in a posting on R-sig-geo: https://stat.ethz.ch/pipermail/r-sig-geo/2011-July/012126.html If any users observe unexpected behaviour following update, please revert to the 0.6-* series, and report with full details to the package maintainer. Extensive checking has been carried out, and no unexpected behaviour observed, but it is not feasible to check all possible use cases, especially erroneous use cases, hence this message. -- Roger Bivand Department of Economics, NHH Norwegian School of Economics, Helleveien 30, N-5045 Bergen, Norway. voice: +47 55 95 93 55; fax +47 55 95 95 43 e-mail: roger.biv...@nhh.no ___ R-packages mailing list r-packa...@r-project.org https://stat.ethz.ch/mailman/listinfo/r-packages __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Unusual graph- modified wind rose perhaps?
In a OpenOffice.org forum someone was asking if the spreadsheet could graph this http://www.elmundo.es/elmundosalud/documentos/2011/06/leche.html I didn't think it could. :) I don't think I've ever seen exactly this layout. Does anyone know if there is anything in R that does a graph like this or that can be adapted to do it. Unfortunately my Spanish is non-existent so I am not sure how effective the graph is in achieving whatever it's suppposed to do. A dot chart might be as effective but it is a flashy graphic. 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] Wrong environment when evaluating and expression?
On Mon, Jul 4, 2011 at 4:11 AM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi All, I have constructed two expressions (e1 e2). I can see that they are not identical, but I cannot figure out how they differ. ### dat - mtcars e1 - expression(with(data = dat, lm(mpg ~ hp))) e2 - as.expression(substitute(with(data = dat, lm(f)), list(f = mpg ~ hp))) str(e1) str(e2) all.equal(e1, e2) identical(e1, e2) # false eval(e1) eval(e2) The context is trying to use a list of formulae to generate several models from a multiply imputed dataset. The package I am using (mice) has methods for with() and that is how I can (easily) get the pooled results. Passing the formula directly does not work, so I was trying to generate the entire call and evaluate it as if I had typed it at the console, but I am missing something (probably rather silly). In e1, mpg ~ hp is a call object but in e2 its a formula with an environment: e1[[1]][[3]][[2]] mpg ~ hp e2[[1]][[3]][[2]] mpg ~ hp class(e1[[1]][[3]][[2]]) [1] call class(e2[[1]][[3]][[2]]) [1] formula environment(e2[[1]][[3]][[2]]) environment: R_GlobalEnv -- 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] Unusual graph- modified wind rose perhaps?
Dear John, You can get pretty close with ggplot2. Best regards, Thierry library(ggplot2) dataset - data.frame(Name = LETTERS[1:26]) dataset$Score - runif(nrow(dataset)) dataset$Category - cut(dataset$Score, breaks = c(-Inf, 0.33, 0.66, Inf), labels = c(Bad, Neutral, Good)) dataset$Name - factor(dataset$Name, levels = dataset$Name[order(dataset$Score)]) dataset$Location - as.numeric(dataset$Name) ggplot(dataset, aes(x = Name, y = Score, fill = Category)) + geom_bar() + coord_polar() #with some extra tweeking dataset - rbind(dataset, data.frame( Location = c(max(dataset$Location) + seq_len(max(dataset$Location) / 2), min(dataset$Location) - seq_len(max(dataset$Location) / 2)), Name = , Score = 0, Category = Good ) ) ggplot(dataset, aes(x = Location, y = Score, fill = Category)) + geom_bar(stat = identity) + coord_polar(start = pi, direction = -1) + scale_fill_manual(value = c(Good = green, Neutral = grey, Bad = red)) + theme_bw() + scale_x_continuous(, breaks = dataset$Location, labels = dataset$Name) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens John Kane Verzonden: maandag 4 juli 2011 13:22 Aan: r-help@r-project.org Onderwerp: [R] Unusual graph- modified wind rose perhaps? In a OpenOffice.org forum someone was asking if the spreadsheet could graph this http://www.elmundo.es/elmundosalud/documentos/2011/06/leche.html I didn't think it could. :) I don't think I've ever seen exactly this layout. Does anyone know if there is anything in R that does a graph like this or that can be adapted to do it. Unfortunately my Spanish is non-existent so I am not sure how effective the graph is in achieving whatever it's suppposed to do. A dot chart might be as effective but it is a flashy graphic. 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] Unusual graph- modified wind rose perhaps?
On 07/04/2011 09:21 PM, John Kane wrote: In a OpenOffice.org forum someone was asking if the spreadsheet could graph this http://www.elmundo.es/elmundosalud/documentos/2011/06/leche.html I didn't think it could. :) I don't think I've ever seen exactly this layout. Does anyone know if there is anything in R that does a graph like this or that can be adapted to do it. Unfortunately my Spanish is non-existent so I am not sure how effective the graph is in achieving whatever it's suppposed to do. A dot chart might be as effective but it is a flashy graphic. Hi John, It's a bit like the function I am working on after the request by Patrick Jemison (radial.pie), and I thought the interactive fill when you sweep the pointer over it is pretty neat. I don't think I'll go that far. I'll let you know when I've got a working function. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Prevent 'R CMD check' from reporting NA/NA_character_ missmatch?
Hello, I'm writing a package am running 'R CMD check' on it. Is there any way to make 'R CMD check' not warn about a missmatch between 'NA_character_' (in the function definition) and 'NA' (in the documentation)? Thanks for any help. Sincerely, Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Copying to R a rectangular array from a Java class
Hi, can you please tel me how to retrieve String two dimensional array as like sapply? -- View this message in context: http://r.789695.n4.nabble.com/Copying-to-R-a-rectangular-array-from-a-Java-class-tp3486167p3643223.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] loop in optim
Hi
May you help me correct my loop function.
I want optim to estimates al_j; au_j; sigma_j; b_j by looking at 0 to 20,
21 to 40, 41 to 60 data points.
The final result should have 4 columns of each of the estimates AND 4 rows
of each of 0 to 20, 21 to 40, 41 to 60.
###MY code is
n=20
runs=4
out=matrix(0,nrow=runs)
llik = function(x)
{
al_j=x[1]; au_j=x[2]; sigma_j=x[3]; b_j=x[4]
sum(na.rm=T,
ifelse(a$R_j 0, -log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+al_j-b_j*a$R_m))^2,
ifelse(a$R_j0 , -log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+au_j-b_j*a$R_m))^2,
-log(pnorm(au_j,mean=b_j*a$R_m,sd=sqrt(sigma_j^2))-
pnorm(au_j,mean=b_j*a$R_m,sd=sqrt(sigma_j^2)
)
}
start.par = c(0, 0, 0.01, 1)
out1 = optim(llik, par=start.par, method=Nelder-Mead)
for (i in 1: runs)
{
index_start=20*(i-1)+1
index_end= 20*i
out[i]=out1[index_start:index_end]
}
out
Thank you in advance
Edward
UCT
My data
R_j R_m
-0.0625 0.002320654
0 -0.004642807
0.0 0.005936332
0.032258065 0.001060848
0 0.007114057
0.0156250.005581558
0 0.002974794
0.015384615 0.004215271
0.060606061 0.005073116
0.028571429 -0.006001279
0 -0.002789594
0.01389 0.00770633
0 0.000371663
0.02739726 -0.004224228
-0.04 0.008362539
0 -0.010951605
0 0.004682924
0.01389 0.011839993
-0.01369863 0.004210383
-0.02778-0.04658949
0 0.00987272
-0.057142857-0.062203157
-0.03030303 -0.119177639
0.09375 0.077054642
0 -0.022763619
-0.0571428570.050408775
0 0.024706076
-0.03030303 0.004043701
0.0625 0.004951088
0 -0.005968731
0 -0.038292548
0 0.013381097
0.014705882 0.006424728
-0.014492754-0.020115626
0 -0.004837891
-0.029411765-0.022054654
0.03030303 0.008936428
0.044117647 8.16925E-05
0 -0.004827246
-0.0422535210.004653096
-0.014705882-0.004222151
0.029850746 0.000107267
-0.028985507-0.001783206
0.029850746 -0.006372981
0.014492754 0.005492374
-0.028571429-0.009005846
0 0.001031683
0.044117647 0.002800551
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[R] Protecting R code
Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. I am searching for ways to protect R code. I would like to create a .exe kind of file which could be executed without using R or requiring to install R. I would not like the R code to be loaded in R. This is so because, after R loads a function, if you type the function name on the command prompt, you can see the complete code. I would not like to give this type of access to the R code. I explored the option of creating .bat file (using command: R CMD BAT) and byte code (using command: compile). These are not useful since they open R, load these functions and then the R code is visible. Is there any other way to protect the R code which would help me package all my files/source files and give me an executable file which would be run without opening R? Another problem is that R is freely downloadable. Is it somehow possible to protect the code from being loaded in R and being seen. Thanks -- Vaishali =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] How to build a matrix of number of appearance?
I have a matrix of claims at year1 that I get simply by claims-read.csv(file=Claims.csv) qq1-claims[claims$Year==Y1,] I have MemberID and ProviderID for every claim in qq1 both are integers An example for the type of questions that I want to answer is how many times ProviderID number 345 appears together with MemberID 23 in the table qq1 In order to answer these questions for every possible ProviderId and every possible MemberID I would like to have a matrix that has first column as memberID when every memberID in qq1 appears only once and columns that have number of appearance of ProviderID==i for every i that has sum(qq1$ProviderID==i)0 My question is if there is a simple way to do it in R Thanks in Advance Uri -- View this message in context: http://r.789695.n4.nabble.com/How-to-build-a-matrix-of-number-of-appearance-tp3643248p3643248.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] writeLines + foreach/doMC
Hi
I'm processing sequencing data trying to collapsing the locations of each
unique sequence and write the results to a file (as storing that in a table
will require 10GB mem at least)
so I wrote a function that, given a sequence id, provide the needed line to
be stored
library(doMC) # load library
registerDoMC(12) # assign the Number of CPU
fileConn-file(paste(fq_file,_SeqID.txt,sep=),open = at) # open
connection
writeLines(paste(ReadID,Freq,Seq,LOC_UG,Nb_UG_Seq,sep=\t),
fileConn) # write header
foreach(i=1:length(uniq.Seq)) %dopar% # for eqch unique sequence
{
writeLines(paste(gettable1(uniq.Seq[i]),collapse= ), fileConn) #write
the the results line
}
close(fileConn)
the code excute well, but the problem is that some lines are wired:
The header and lot of lines are ok :
ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:16:9530:21025#ATGC/1 2
X_10130:489:+,X_10130:489:+ 2
HWI-EA332_0036:5:117:6674:4940#ATGC/1 1
X:432:-,X:432:- 2
HWI-EA332_0036:5:62:15592:7375#ATGC/1 2
X_22660:253:+,X_22660:253:+ 2
HWI-EA332_0036:5:110:14349:8422#ATGC/1 4
X_13806:399:+,X_13806:399:+,X_27263:481:+,X_27263:481:+ 4
other looks wired
HWI-EA332_0036:5:17:1400ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:61:7734:4201ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:117:5361:10666#ATGReadIDFreqSeqLOC_UG
Nb_UG_Seq
HWI-EA332_0036:5:115:7421:20664#ATGC/1 GATCReadIDFreqSeq
LOC_UGNb_UG_Seq
HWI-EA332_0036:5:175:95:- 2
HWI-EA332_0036:5JCVI_35536:444:+ 2
X 1 X_22484:571:-,X_22484:571:- 2
Is this due to the fact that one process start to write prior the other has
finished ?
Is there a way to solve this problem ?
Any suggestions would be greatly appreciated.
Thanks and have a nice day.
Best,
Ramzi TEMANNI
http://www.linkedin.com/in/ramzitemanni
[[alternative HTML version deleted]]
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] wavelets
From: jdnew...@dcn.davis.ca.us Date: Mon, 4 Jul 2011 00:45:41 -0700 To: tyagi...@gmail.com; r-help@r-project.org Subject: Re: [R] wavelets Study the topic more carefully, I suppose. My understanding is that wavelets do not in themselves compress anything, but because they sort out the interesting data from the uninteresting data, it can be easy to toss the uninteresting data (lossy data compression). Perhaps you should understand better what your Matlab library is doing. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. user123 tyagi...@gmail.com wrote: I'm new to the topic of wavelets. When I tried to use the mra function in the wavelets package, the data is not getting compressed. eg. if the original data has 500 values , the output data also has the same. However in MATLAB, depending on the level of decompositon, the data gets compressed. How do I implement this in R? can you post some code? You can always compress into one value of course by turning bytes into a single char string, what you want is entropy. I posted some example code before and I remember it took effort to not get the subsampling. mra is probably multi-resolution analysis and I'd suppose you want all the samples. You probably need paper and pencil however at this point. -- View this message in context: http://r.789695.n4.nabble.com/wavelets-tp3642973p3642973.html Sent from the R help mailing list archive at Nabble.com. _ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Prevent 'R CMD check' from reporting NA/NA_character_ missmatch?
On Mon, 4 Jul 2011, Johannes Graumann wrote: Hello, I'm writing a package am running 'R CMD check' on it. Is there any way to make 'R CMD check' not warn about a missmatch between 'NA_character_' (in the function definition) and 'NA' (in the documentation)? Be consistent Why do you want incorrect documentation of your package? (It is not clear of the circumstances here: normally 1 vs 1L and similar are not reported if they are the only errors.) And please do note the posting guide - this is not really the correct list - you were asked to give an actual example with output. -- Brian D. Ripley, rip...@stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] writeLines + foreach/doMC
Read something about parallel processing and how I/O should be done by a
single process.
Suggestion: write a different file from each thread then combine the
results with cat or similar.
Hope it helps
mario
On 04-Jul-11 11:58, Ramzi TEMANNI wrote:
Hi
I'm processing sequencing data trying to collapsing the locations of each
unique sequence and write the results to a file (as storing that in a table
will require 10GB mem at least)
so I wrote a function that, given a sequence id, provide the needed line to
be stored
library(doMC) # load library
registerDoMC(12) # assign the Number of CPU
fileConn-file(paste(fq_file,_SeqID.txt,sep=),open = at) # open
connection
writeLines(paste(ReadID,Freq,Seq,LOC_UG,Nb_UG_Seq,sep=\t),
fileConn) # write header
foreach(i=1:length(uniq.Seq)) %dopar% # for eqch unique sequence
{
writeLines(paste(gettable1(uniq.Seq[i]),collapse= ), fileConn) #write
the the results line
}
close(fileConn)
the code excute well, but the problem is that some lines are wired:
The header and lot of lines are ok :
ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:16:9530:21025#ATGC/1 2
X_10130:489:+,X_10130:489:+ 2
HWI-EA332_0036:5:117:6674:4940#ATGC/1 1
X:432:-,X:432:- 2
HWI-EA332_0036:5:62:15592:7375#ATGC/1 2
X_22660:253:+,X_22660:253:+ 2
HWI-EA332_0036:5:110:14349:8422#ATGC/1 4
X_13806:399:+,X_13806:399:+,X_27263:481:+,X_27263:481:+ 4
other looks wired
HWI-EA332_0036:5:17:1400ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:61:7734:4201ReadIDFreqSeqLOC_UGNb_UG_Seq
HWI-EA332_0036:5:117:5361:10666#ATGReadIDFreqSeqLOC_UG
Nb_UG_Seq
HWI-EA332_0036:5:115:7421:20664#ATGC/1 GATCReadIDFreqSeq
LOC_UGNb_UG_Seq
HWI-EA332_0036:5:175:95:- 2
HWI-EA332_0036:5JCVI_35536:444:+ 2
X 1 X_22484:571:-,X_22484:571:- 2
Is this due to the fact that one process start to write prior the other has
finished ?
Is there a way to solve this problem ?
Any suggestions would be greatly appreciated.
Thanks and have a nice day.
Best,
Ramzi TEMANNI
http://www.linkedin.com/in/ramzitemanni
[[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.
--
Ing. Mario Valle
Data Analysis and Visualization Group| http://www.cscs.ch/~mvalle
Swiss National Supercomputing Centre (CSCS) | Tel: +41 (91) 610.82.60
v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax: +41 (91) 610.82.82
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] extracting data
Thanks! That works well. Best, Ana From: Peter Ehlers ehl...@ucalgary.ca To: Ana Kolar annako...@yahoo.com Cc: Sarah Goslee sarah.gos...@gmail.com; R r-help@r-project.org Sent: Tuesday, 28 June 2011, 19:37 Subject: Re: [R] extracting data On 2011-06-28 09:54, Ana Kolar wrote: Hi Sarah, Thank you for your response. Here is a toy example: library(MatchIt) data(lalonde) A-lalonde f-treat ~ age + I(age^2) + educ + I(educ^2) + black + hispan + married + nodegree + re74 + I(re74^2) + re75 + I(re75^2) m-nearest m.out.base- matchit(formula=f, data=A, method=m) B- match.data(m.out.base) An- nrow(A) Bn- nrow(B) Cn- An - Bn C- ?? Can't you just use idx - setdiff(rownames(A), rownames(B)) C - A[idx, ] Peter Ehlers From: Sarah Gosleesarah.gos...@gmail.com To: Ana Kolarannako...@yahoo.com Cc: Rr-help@r-project.org Sent: Tuesday, 28 June 2011, 18:44 Subject: Re: [R] extracting data Hi Ana, On Tue, Jun 28, 2011 at 12:28 PM, Ana Kolarannako...@yahoo.com wrote: Let's say I have an original data set which is called A and data extracted from this original data set, called B. Based on these A and B data set I would like to get data set C which includes all the remaining data from the data set A after we exclude data of the data set B. Any idea how to do this? Yes. Several. But to know which one to suggest, I need to know more about your data. How about a toy example, so the list members can see your index variables, etc? Or how you created the subset B, and why you can't just use the opposite of that procedure? Sarah -- Sarah Goslee http://www.functionaldiversity.org [[alternative HTML version deleted]] [[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] Unusual graph- modified wind rose perhaps?
Very pretty Thierry, I was wondering if ggplot2 could do something like it but my knowledge of ggplot2 is far to little to attempt it myself. I'm going to really have to spend some time on that code. Thanks --- On Mon, 7/4/11, ONKELINX, Thierry thierry.onkel...@inbo.be wrote: From: ONKELINX, Thierry thierry.onkel...@inbo.be Subject: RE: [R] Unusual graph- modified wind rose perhaps? To: John Kane jrkrid...@yahoo.ca, r-help@r-project.org r-help@r-project.org Received: Monday, July 4, 2011, 8:14 AM Dear John, You can get pretty close with ggplot2. Best regards, Thierry library(ggplot2) dataset - data.frame(Name = LETTERS[1:26]) dataset$Score - runif(nrow(dataset)) dataset$Category - cut(dataset$Score, breaks = c(-Inf, 0.33, 0.66, Inf), labels = c(Bad, Neutral, Good)) dataset$Name - factor(dataset$Name, levels = dataset$Name[order(dataset$Score)]) dataset$Location - as.numeric(dataset$Name) ggplot(dataset, aes(x = Name, y = Score, fill = Category)) + geom_bar() + coord_polar() #with some extra tweeking dataset - rbind(dataset, data.frame( Location = c(max(dataset$Location) + seq_len(max(dataset$Location) / 2), min(dataset$Location) - seq_len(max(dataset$Location) / 2)), Name = , Score = 0, Category = Good ) ) ggplot(dataset, aes(x = Location, y = Score, fill = Category)) + geom_bar(stat = identity) + coord_polar(start = pi, direction = -1) + scale_fill_manual(value = c(Good = green, Neutral = grey, Bad = red)) + theme_bw() + scale_x_continuous(, breaks = dataset$Location, labels = dataset$Name) ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek team Biometrie Kwaliteitszorg Gaverstraat 4 9500 Geraardsbergen Belgium Research Institute for Nature and Forest team Biometrics Quality Assurance Gaverstraat 4 9500 Geraardsbergen Belgium tel. + 32 54/436 185 thierry.onkel...@inbo.be www.inbo.be To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey -Oorspronkelijk bericht- Van: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] Namens John Kane Verzonden: maandag 4 juli 2011 13:22 Aan: r-help@r-project.org Onderwerp: [R] Unusual graph- modified wind rose perhaps? In a OpenOffice.org forum someone was asking if the spreadsheet could graph this http://www.elmundo.es/elmundosalud/documentos/2011/06/leche.html I didn't think it could. :) I don't think I've ever seen exactly this layout. Does anyone know if there is anything in R that does a graph like this or that can be adapted to do it. Unfortunately my Spanish is non-existent so I am not sure how effective the graph is in achieving whatever it's suppposed to do. A dot chart might be as effective but it is a flashy graphic. 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] cumulative incidence plot vs survival plot
Note that most of the nonparametric and semi-parametric competing risks analyses can be performed within the survival package. This includes nonparametric estimation of cause-specific cumulative incidence curves and the log-rank type test. It suffices to create a weighted data set as explained in Geskus, Biometrics 67, p. 39-49, 2011. Ronald Geskus Academic Medical Center Amsterdam, the Netherlands Hi, I am wondering if anyone can explain to me if cumulative incidence (CI) is The cumulative incidence curve and the KM are not the same, when there are multiple outcomes. See the etype argument to survfit, which is used to create CI curves (?survfit.formula). For testing differences between CI curves use the cmprsk library from Gray; it can also draw curves by the survfit routine has a lot more flexibility. -- View this message in context: http://r.789695.n4.nabble.com/cumulative-incidence-plot-vs-survival-plot-tp3628772p3643659.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] Protecting R code
On 04.07.2011 09:47, Vaishali Sadaphal wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. I am searching for ways to protect R code. I would like to create a .exe kind of file which could be executed without using R or requiring to install R. I would not like the R code to be loaded in R. This is so because, after R loads a function, if you type the function name on the command prompt, you can see the complete code. I would not like to give this type of access to the R code. I explored the option of creating .bat file (using command: R CMD BAT) and byte code (using command: compile). These are not useful since they open R, load these functions and then the R code is visible. Is there any other way to protect the R code which would help me package all my files/source files and give me an executable file which would be run without opening R? Another problem is that R is freely downloadable. Is it somehow possible to protect the code from being loaded in R and being seen. H, R is open source software under the GPL (which is infective) and designed as such. Good luck it is almost impossible to hide the source code in R. And people who tried to generate C based binary packages found those can only be used under a small subset of platforms with few versions of R. Since R is distributed under the GPL: When you write code and make it available to others, you should be aware of this fact that you may have to distribute the sources under GPL as well - under some circumstances your lawyer can explain much better than I. Thanks -- Vaishali =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If it is confidential or privileged information, you should not send it to a mailing list where the archives are published. Best, Uwe Ligges If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[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] Protecting R code
On Mon, Jul 4, 2011 at 8:47 AM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. At some point the R code has to be run. Which means it has to be read by an interpreter that can handle R code. Which means, unless you rewrite the interpreter, the R code must exist as such. Even if you could compile R into C code into machine code and distribute a .exe file, its still possible in theory to reverse-engineer it and get something like the original back - the original logic if not the original names of the variables and functions. You could rewrite the interpreter to only run encrypted, signed code that requires a decryption key, but you still have to give the user the decryption key at some point in order to get the plaintext code. Again, its an obfuscation problem of hiding the key somewhere, and hence is going to fail. It all depends on how much expense you want to go to in order to make the expense of circumventing your solution more than its worth. Tell me how much that is, and I will tell you the solution. For total security[1], you need to run the code on servers YOU control, and only give access via a network API. You can do this with RServe or any of the HTTP-based systems like Rapache. Barry [1] Except of course servers can be hacked or socially-engineered into. For total security, disconnect your machine from the network and from any power supply. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 build a matrix of number of appearance?
On Jul 4, 2011, at 5:48 AM, UriB wrote: I have a matrix of claims at year1 that I get simply by claims-read.csv(file=Claims.csv) qq1-claims[claims$Year==Y1,] I have MemberID and ProviderID for every claim in qq1 both are integers An example for the type of questions that I want to answer is how many times ProviderID number 345 appears together with MemberID 23 in the table qq1 In order to answer these questions for every possible ProviderId and every possible MemberID I would like to have a matrix that has first column as memberID when every memberID in qq1 appears only once and columns that have number of appearance of ProviderID==i for every i that has sum(qq1$ProviderID==i)0 My question is if there is a simple way to do it in R A really quick way of finding this would be: as.data.frame ( xtabs( ~ ProviderID +MemberID, data= qq1) ) -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Protecting R code
On 7/4/2011 7:28 AM, Uwe Ligges wrote: On 04.07.2011 09:47, Vaishali Sadaphal wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. I am searching for ways to protect R code. I would like to create a .exe kind of file which could be executed without using R or requiring to install R. I would not like the R code to be loaded in R. This is so because, after R loads a function, if you type the function name on the command prompt, you can see the complete code. I would not like to give this type of access to the R code. I explored the option of creating .bat file (using command: R CMD BAT) and byte code (using command: compile). These are not useful since they open R, load these functions and then the R code is visible. Is there any other way to protect the R code which would help me package all my files/source files and give me an executable file which would be run without opening R? Another problem is that R is freely downloadable. Is it somehow possible to protect the code from being loaded in R and being seen. H, R is open source software under the GPL (which is infective) and designed as such. Good luck it is almost impossible to hide the source code in R. And people who tried to generate C based binary packages found those can only be used under a small subset of platforms with few versions of R. Since R is distributed under the GPL: When you write code and make it available to others, you should be aware of this fact that you may have to distribute the sources under GPL as well - under some circumstances your lawyer can explain much better than I. Linux is distributed under the GPL, and people distribute software implemented in Linux without having to release their source code. There are different versions of the GPL. You should read them carefully and consult with an attorney. However, if you honestly read the GPL verbiage, you may find that you know more than your attorney -- but you still need the attorney. I'm not an attorney and I haven't read GPL verbiage in a while, but as I recall a key issue is whether your code is your creation or a modification of some other GPL code. If the latter, you could lose in court if challenged. I see two options: 1. Write the proprietary portion of your code in a compiled language like C, C++, or Fortran, and link from R to your compiled subroutines. If you do not already write R packages, I strongly urge you to first learn how to produce and use R packages. Documentation on Creating R Packages is available from any standard CRAN mirror. I suggest you create separate R packages (with different names) complete with documentation for your internal only version in R only and for your public version that uses compiled code. This allows you to prototype your new ideas quickly in R before you spend the money to convert them to compiled code. It also encourages you to build test cases in a way that increases software quality. Then you can distribute the public R package in its standard compiled format, which your users can install using the standard procedure to Install package(s) from local zip file (available on the Packages menu in Rgui). This is arguably the cleanest legally, because then it's clear that your proprietary code has an existence independent of R. You can distribute your package with an appropriate end user license agreement and instructions for how to install R and any CRAN packages you use plus your own code. 2. You can write something to encrypt your R code. I know someone who has done this. However, the legal status is not as clean as if you wrote you proprietary algorithm in a compiled language, because if someone with a larger budget for attorneys wants to take you to court demanding your source code, you might lose. I doubt if that would happen, but I'm not an attorney, so I don't know. I do know that people often lose legal battles just because their opponents have much better attorneys. The advantage of this is that you could then distribute your latest changes immediately after you get them working. Another disadvantage is that your code will have to decrypt the R code prior to running it, which means that your code might still be available to anyone clever enough to interrupt your code while it's running. Thus, it's not as secure as writing compiled code, in addition to not having as strong a claim to having an existence independent of R. You could also combine this with the first, where your latest release would encrypt your latest enhancements while you are working to translate those into compiled code. Few people with university appointments have to worry about these issues, because they get paid for generating new knowledge and sharing it with
Re: [R] Protecting R code
Hello: On 7/4/2011 7:41 AM, Barry Rowlingson wrote: On Mon, Jul 4, 2011 at 8:47 AM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. At some point the R code has to be run. Which means it has to be read by an interpreter that can handle R code. Which means, unless you rewrite the interpreter, the R code must exist as such. Even if you could compile R into C code into machine code and distribute a .exe file, its still possible in theory to reverse-engineer it and get something like the original back - the original logic if not the original names of the variables and functions. You could rewrite the interpreter to only run encrypted, signed code that requires a decryption key, but you still have to give the user the decryption key at some point in order to get the plaintext code. Again, its an obfuscation problem of hiding the key somewhere, and hence is going to fail. It all depends on how much expense you want to go to in order to make the expense of circumventing your solution more than its worth. Tell me how much that is, and I will tell you the solution. For total security[1], you need to run the code on servers YOU control, and only give access via a network API. You can do this with RServe or any of the HTTP-based systems like Rapache. An organization I know that encrypted R code started with making it available only on their servers. This was maybe four years ago. I'm not sure what they do now, but I think they have since lost their major proponents of R internally and have probably translated all the code they wanted to sell into a compiled language in a way that didn't require R at all. Spencer Barry [1] Except of course servers can be hacked or socially-engineered into. For total security, disconnect your machine from the network and from any power supply. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] modification of cross-validations in rpart
Hello, I am using the rpart function (from the rpart package) to do a regression tree that would describe the behaviour of a fish species according to several environmental variables. For each fish (sampling unit), I have repeated observations of the response variable, which means that the data are not independent. Normally, in this case, V-fold cross-validation needs to be modified to prevent over-optimistic predictions of error rates by cross-validation and overestimation of the tree size. A way to overcome this problem is by selecting only whole sampling units in our subsets of cross-validation. My problem is that I dont know how to perform this modification of the cross-validation process in the rpart function. Is there a way to do this modification in rpart or is there any other function I could use that would consider interdependence in the response variable? Here is an example of the code I am using (Y being the response variable and data.env being a data frame of the environmental variables): Tree = rpart(Y ~ X1 + X2 + X3,xval=100,data=data.env) Thanks Katerine [[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] I need help for creating a timevar
Hi all! I have data in „Long“ format which I would like to reshape to „Wide“. I know that one possibility is the „reshape“ command, which needs a „timevar“. Data look as follows: There are approx. 3000 persons („IDENTITY“) and, for each person, there are between 2 and 20 events („EVENT“). For now, there's one row for each event (9506 rows) http://r.789695.n4.nabble.com/file/n3643658/Screenshot-2.png What is missing is the „timevar“ (SPSS calls it „INDEX“), which numbers the events WITHIN each person (right column). I managed to number the events from 1 to 9506 with the seq-command, first writing the number of rows in nEVENT: number -seq(file=event, 1, nEVENT, b=1) Yet, I didn't manage to do so for each individual separately. I guess it would be possible with the „split“ command, but I can't figure out how to apply it. Can anyone give me a hint? Thank you! Karen -- View this message in context: http://r.789695.n4.nabble.com/I-need-help-for-creating-a-timevar-tp3643658p3643658.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] Protecting R code
Hey All, Thank you so much for quick replies. Looks like translation to C/C++ is the only robust option. Do you think there exists any ready-made R to C translator? Thanks -- Vaishali Vaishali Paithankar Sadaphal Tata Consultancy Services Mailto: vaishali.sadap...@tcs.com Website: http://www.tcs.com Experience certainty. IT Services Business Solutions Outsourcing From: Spencer Graves spencer.gra...@prodsyse.com To: Barry Rowlingson b.rowling...@lancaster.ac.uk Cc: Vaishali Sadaphal vaishali.sadap...@tcs.com, r-help@r-project.org Date: 07/04/2011 08:42 PM Subject: Re: [R] Protecting R code Hello: On 7/4/2011 7:41 AM, Barry Rowlingson wrote: On Mon, Jul 4, 2011 at 8:47 AM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. At some point the R code has to be run. Which means it has to be read by an interpreter that can handle R code. Which means, unless you rewrite the interpreter, the R code must exist as such. Even if you could compile R into C code into machine code and distribute a .exe file, its still possible in theory to reverse-engineer it and get something like the original back - the original logic if not the original names of the variables and functions. You could rewrite the interpreter to only run encrypted, signed code that requires a decryption key, but you still have to give the user the decryption key at some point in order to get the plaintext code. Again, its an obfuscation problem of hiding the key somewhere, and hence is going to fail. It all depends on how much expense you want to go to in order to make the expense of circumventing your solution more than its worth. Tell me how much that is, and I will tell you the solution. For total security[1], you need to run the code on servers YOU control, and only give access via a network API. You can do this with RServe or any of the HTTP-based systems like Rapache. An organization I know that encrypted R code started with making it available only on their servers. This was maybe four years ago. I'm not sure what they do now, but I think they have since lost their major proponents of R internally and have probably translated all the code they wanted to sell into a compiled language in a way that didn't require R at all. Spencer Barry [1] Except of course servers can be hacked or socially-engineered into. For total security, disconnect your machine from the network and from any power supply. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[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] Protecting R code
Put it on rapache or otherwise server but this seems like a waste depending on what you are doing Server side is only good way but making c++ may be interesting test Sent from my Verizon Wireless BlackBerry -Original Message- From: Vaishali Sadaphal vaishali.sadap...@tcs.com Date: Mon, 4 Jul 2011 16:48:13 To: spencer.gra...@prodsyse.com Cc: r-help@r-project.org; b.rowling...@lancaster.ac.uk Subject: Re: [R] Protecting R code Hey All, Thank you so much for quick replies. Looks like translation to C/C++ is the only robust option. Do you think there exists any ready-made R to C translator? Thanks -- Vaishali Vaishali Paithankar Sadaphal Tata Consultancy Services Mailto: vaishali.sadap...@tcs.com Website: http://www.tcs.com Experience certainty. IT Services Business Solutions Outsourcing From: Spencer Graves spencer.gra...@prodsyse.com To: Barry Rowlingson b.rowling...@lancaster.ac.uk Cc: Vaishali Sadaphal vaishali.sadap...@tcs.com, r-help@r-project.org Date: 07/04/2011 08:42 PM Subject: Re: [R] Protecting R code Hello: On 7/4/2011 7:41 AM, Barry Rowlingson wrote: On Mon, Jul 4, 2011 at 8:47 AM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. At some point the R code has to be run. Which means it has to be read by an interpreter that can handle R code. Which means, unless you rewrite the interpreter, the R code must exist as such. Even if you could compile R into C code into machine code and distribute a .exe file, its still possible in theory to reverse-engineer it and get something like the original back - the original logic if not the original names of the variables and functions. You could rewrite the interpreter to only run encrypted, signed code that requires a decryption key, but you still have to give the user the decryption key at some point in order to get the plaintext code. Again, its an obfuscation problem of hiding the key somewhere, and hence is going to fail. It all depends on how much expense you want to go to in order to make the expense of circumventing your solution more than its worth. Tell me how much that is, and I will tell you the solution. For total security[1], you need to run the code on servers YOU control, and only give access via a network API. You can do this with RServe or any of the HTTP-based systems like Rapache. An organization I know that encrypted R code started with making it available only on their servers. This was maybe four years ago. I'm not sure what they do now, but I think they have since lost their major proponents of R internally and have probably translated all the code they wanted to sell into a compiled language in a way that didn't require R at all. Spencer Barry [1] Except of course servers can be hacked or socially-engineered into. For total security, disconnect your machine from the network and from any power supply. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[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] forecast: bias in sampling from seasonal Arima model?
Dear all, I stumbled upon what appears to be a troublesome issue when sampling from an ARIMA model (from Rob Hyndman's excellent 'forecast' package) that contains a seasonal AR component. Here's how to reproduce the issue. (I'm using R 2.9.2 with forecast 2.19; see sessionInfo() below). First some data: x - c( 0.132475, 0.143119, 0.108104, 0.247291, 0.029510, -0.119591, -0.133313, -0.098128, 0.192698, 0.110328, 0.163671, -0.004925, -0.239209, -0.055122, -0.051121, 0.154108, 0.008665, -0.074702, 0.066534, -0.098728, -0.068668, 0.150935, -0.022547, 0.028625, 0.107092, -0.065396, -0.253247, -0.115240, -0.113535, -0.064191, -0.006032, 0.039233, 0.129013, -0.068462, 0.022398, -0.052427, -0.005586, 0.011447, -0.022667, -0.120536, -0.234398, -0.164087, -0.177160, -0.120624, -0.025104, 0.001144, -0.193424, -0.260674, -0.036976, -0.009590, -0.004920, 0.130545, 0.120527, 0.041121, -0.123321, 0.023836, -0.188418, 0.015807, -0.056012, 0.000496, 0.051806, -0.067574, 0.012775, 0.244083, 0.148857, 0.013874, 0.235252, 0.151935, 0.036986, 0.134482, -0.003359, -0.019422, 0.086195, 0.206569, 0.123565, 0.070835, -0.183189, -0.046513, 0.071920, -0.038360, 0.135293, 0.054746, -0.280340, 0.110638, 0.009729, 0.115541, 0.021397, 0.097835, -0.028434, -0.218416, 0.044552, 0.442563, 0.084317, 0.044149, 0.201100, 0.076112, -0.134955, 0.023870, 0.077111, 0.085490, 0.023154, 0.099757, -0.026509, -0.189839, 0.026614, 0.184916, -0.007266, 0.081276, 0.312526, 0.051199, -0.104707, -0.004206, 0.062440, 0.126385, -0.018100, 0.092513, 0.186459, -0.170184, -0.126168, 0.122739, 0.097495, 0.008633, -0.034519, 0.187264, -0.153409, 0.009440, 0.150561, 0.067744, 0.045129, 0.230831, -0.079700, -0.162694, -0.044251, -0.007663, 0.048986, 0.065724, 0.159706, 0.040067, -0.059949, 0.024810, -0.154852, 0.018080, 0.165935, 0.203050, 0.011035, -0.232585, -0.162248, -0.104872, -0.062516, -0.089766, 0.100304, 0.142170, -0.144969, -0.032500, -0.002131, 0.165890, 0.107629, 0.075752, 0.119003, 0.095955, 0.039842, 0.081208, 0.348529, 0.145694, -0.210700, 0.384966, -0.054503, 0.293329, 0.184295, 0.368986, 0.135270, 0.124917, 0.185286, -0.252088, -0.169708, -0.010204, 0.021934, 0.003572, 0.180148, 0.075836, -0.232065, -0.127255, -0.147122, 0.056163, 0.067004, 0.217810, 0.074513, -0.167389, 0.172578, -0.148127, 0.057025, 0.042623, 0.094214, 0.047004, -0.345453, -0.265104, -0.082897, 0.052705, -0.067002, 0.191941, 0.010989, -0.298567, -0.162841, 0.043773, 0.185459, 0.126305, 0.383101, 0.092747, -0.368453, -0.325097, 0.029564, -0.015390, 0.013807, 0.152062, -0.047015, -0.429245, -0.097742, 0.104502, -0.007547, -0.000245, 0.062830, 0.030093, -0.381043, -0.267704, -0.125930, -0.032264, -0.041657, 0.040073, 0.084431, -0.276316, -0.305253, -0.019942, 0.045390, 0.046090, 0.145700, 0.069920, -0.210079, 0.050967, 0.042283, 0.248840, 0.007883, 0.203171, 0.050722, -0.109773, -0.110301, -0.095433, 0.071133, 0.023793, 0.192476, 0.057746) First, a CORRECT model, containing a seasonal MA component but no seasonal AR component. After estimation, I forecast for 1 time-step, and I take the mean of sampling 1 times from the same model: my.arima1 - Arima(x, order=c(3,0,0), seasonal=list(order=c(0,0,2), period=7), include.mean=FALSE) forecast(my.arima1, 1) Point Forecast Lo 80 Hi 80 Lo 95 Hi 95 251-0.03143283 -0.1882245 0.1253589 -0.271225 0.2083594 set.seed(1827) ; mean(sapply(seq_len(1), function(i) as.numeric(simulate(my.arima1, 1)) )) [1] -0.03258454 The results (Point Forecast versus the output of mean()) are identical to some sampling error. Now the INCORRECT model arises from adding one seasonal AR component: my.arima2 - Arima(x, order=c(3,0,0), seasonal=list(order=c(1,0,2), period=7), include.mean=FALSE) forecast(my.arima2, 1) Point Forecast Lo 80 Hi 80 Lo 95 Hi 95 251 -0.1848579 -0.322421 -0.04729492 -0.3952424 0.02552655 set.seed(1827) ; mean(sapply(seq_len(1), function(i) as.numeric(simulate(my.arima2, 1)) )) [1] -0.05416299 For the results are substantially different (-0.18 versus -0.05), and the latter does not change much if I take a much bigger sample. Did anybody encounter this in the past? Is this a bug? For reference, here are the results of sessionInfo(): sessionInfo() R version 2.9.2 (2009-08-24) x86_64-pc-linux-gnu locale: C attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] KernSmooth_2.23-3 digest_0.4.2 forecast_2.19 fracdiff_1.3-2 [5] tseries_0.10-12zoo_1.4-0 quadprog_1.4-11glmnet_1.7 [9] Matrix_0.999375-30 biglm_0.7 DBI_0.2-4 inline_0.3.7 [13] XML_2.6-0 timeSeries_2110.86 timeDate_2110.87 RODBC_1.3-2 [17] reshape_0.8.3 plyr_0.1.9 MASS_7.2-48nnet_7.2-48 [21]
[R] Rpad library
can anyone help me with a well documented tutorial on Rpad package? I need to do HTML programming in R.Can anyone help me with a tutorial? -- View this message in context: http://r.789695.n4.nabble.com/Rpad-library-tp3644041p3644041.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] For help in R coding
Dear sir,
I have one more problem.Sorry to disturb you again.
I have a data frame like this-
Col1 Col2 Col3 Col4
1 0 14
0 0 02
4 2 00
1 5 00
0 0 43
0 0 02
0 0 00
1 1 05
I want to delete all those rows which have more than two 0s
like in above input row2 has 3 zeros,row6 has 3 zeros and row 7 has 4 zeros.so
i want to exclude them so that my output should be-
Col1 Col2 Col3 Col4
1 0 14
4 2 00
1 5 00
0 0 43
1 1 05
Can you please tell me how to code for this problem?
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, July 04, 2011 2:02 AM
To: Bansal, Vikas
Cc: Dennis Murphy; r-help@r-project.org
Subject: Re: [R] For help in R coding
On Jul 3, 2011, at 6:10 PM, Bansal, Vikas wrote:
So I want to code so that it will give the output like this-
DATA FRAME (Input)
Editing the task so it is reproducible:
dat - read.table(textConnection(' col3 col9
T .a,g,,
A.t,t,,
A.,c,c,
C .,a,,,
G .,t,t,t
A .c,,g,^!.
A .g,ggg.^!,
A .$,.,
C a,g,,t,
T ,.,^!.
T ,$.,.'), header=TRUE,
stringsAsFactors=FALSE)
output
AC GT
1 0 14
4 0 02
4 2 00
1 5 00
0 0 43
It's also possible to apply the logic that Gabor Grothendieck offered
at the beginning of this thread:
dat[, newcol] - apply(dat, 1, function(x) gsub(\\,|\\. ,x[1],
x[2]) )
# ... and the obvious repetition for C.G.T
dat[,A] - nchar( gsub([^aA], , dat[ , newcol] ))
dat
col3 col9 newcol A
1 T .a,g,, TaTgTT 1
2 A .t,t,, AtAtAA 4
3 A .,c,c, AAcAcA 4
4 C .,a,,, CCaCCC 1
5 G.,t,t,tGGtGtGt 0
6 A .c,,g,^!. AcAAgA^!A 5
7 A .g,ggg.^!, AgAgggA^!A 4
8 A .$,., A$AAA 8
9 Ca,g,,t,aCgCCtC 1
10T ,.,^!. TTT^!T 0
11T ,$.,. T$TTT 0
I am deeply in debt to Gabor Grothendieck. He taught me all I know
regarding regex. The man is a master at patterns.
--
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Wrong environment when evaluating and expression?
Thanks Gabor, that makes sense now. In case anyone else runs into something similar, I ended up just passing a character string of the formula so it could be coerced to a formula in the correct environment. Thanks again, Josh On Mon, Jul 4, 2011 at 4:26 AM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Mon, Jul 4, 2011 at 4:11 AM, Joshua Wiley jwiley.ps...@gmail.com wrote: Hi All, I have constructed two expressions (e1 e2). I can see that they are not identical, but I cannot figure out how they differ. ### dat - mtcars e1 - expression(with(data = dat, lm(mpg ~ hp))) e2 - as.expression(substitute(with(data = dat, lm(f)), list(f = mpg ~ hp))) str(e1) str(e2) all.equal(e1, e2) identical(e1, e2) # false eval(e1) eval(e2) The context is trying to use a list of formulae to generate several models from a multiply imputed dataset. The package I am using (mice) has methods for with() and that is how I can (easily) get the pooled results. Passing the formula directly does not work, so I was trying to generate the entire call and evaluate it as if I had typed it at the console, but I am missing something (probably rather silly). In e1, mpg ~ hp is a call object but in e2 its a formula with an environment: e1[[1]][[3]][[2]] mpg ~ hp e2[[1]][[3]][[2]] mpg ~ hp class(e1[[1]][[3]][[2]]) [1] call class(e2[[1]][[3]][[2]]) [1] formula environment(e2[[1]][[3]][[2]]) environment: R_GlobalEnv -- Statistics Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] For help in R coding
On Jul 4, 2011, at 1:29 PM, Bansal, Vikas wrote:
Dear sir,
I have one more problem.Sorry to disturb you again.
I have a data frame like this-
Col1 Col2 Col3 Col4
1 0 14
0 0 02
4 2 00
1 5 00
0 0 43
0 0 02
0 0 00
1 1 05
I want to delete all those rows which have more than two 0s
like in above input row2 has 3 zeros,row6 has 3 zeros and row 7 has
4 zeros.so i want to exclude them so that my output should be-
Col1 Col2 Col3 Col4
1 0 14
4 2 00
1 5 00
0 0 43
1 1 05
Can you please tell me how to code for this problem?
I am having a difficult time figuring out why this is not an obvious
application for `apply` and [ using logical indexing. I suggest you
do some more self-study with the introductory material that you will
find here:
http://cran.r-project.org/other-docs.html
(It also is a frequently asked question, so searching the archives for
worked examples should also be considered.)
Using search terms delete all rows with ==
http://search.r-project.org/cgi-bin/namazu.cgi?query=delete+rows+with+all+%3D%3Dmax=100result=normalsort=scoreidxname=functionsidxname=Rhelp08idxname=Rhelp10idxname=Rhelp02
--
David.
Thanking you,
Warm Regards
Vikas Bansal
Msc Bioinformatics
Kings College London
From: David Winsemius [dwinsem...@comcast.net]
Sent: Monday, July 04, 2011 2:02 AM
To: Bansal, Vikas
Cc: Dennis Murphy; r-help@r-project.org
Subject: Re: [R] For help in R coding
On Jul 3, 2011, at 6:10 PM, Bansal, Vikas wrote:
So I want to code so that it will give the output like this-
DATA FRAME (Input)
Editing the task so it is reproducible:
dat - read.table(textConnection(' col3 col9
T .a,g,,
A.t,t,,
A.,c,c,
C .,a,,,
G .,t,t,t
A .c,,g,^!.
A .g,ggg.^!,
A .$,.,
C a,g,,t,
T ,.,^!.
T ,$.,.'), header=TRUE,
stringsAsFactors=FALSE)
output
AC GT
1 0 14
4 0 02
4 2 00
1 5 00
0 0 43
It's also possible to apply the logic that Gabor Grothendieck offered
at the beginning of this thread:
dat[, newcol] - apply(dat, 1, function(x) gsub(\\,|\\. ,x[1],
x[2]) )
# ... and the obvious repetition for C.G.T
dat[,A] - nchar( gsub([^aA], , dat[ , newcol] ))
dat
col3 col9 newcol A
1 T .a,g,, TaTgTT 1
2 A .t,t,, AtAtAA 4
3 A .,c,c, AAcAcA 4
4 C .,a,,, CCaCCC 1
5 G.,t,t,tGGtGtGt 0
6 A .c,,g,^!. AcAAgA^!A 5
7 A .g,ggg.^!, AgAgggA^!A 4
8 A .$,., A$AAA 8
9 Ca,g,,t,aCgCCtC 1
10T ,.,^!. TTT^!T 0
11T ,$.,. T$TTT 0
I am deeply in debt to Gabor Grothendieck. He taught me all I know
regarding regex. The man is a master at patterns.
--
David Winsemius, MD
West Hartford, CT
David Winsemius, MD
West Hartford, CT
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to build a matrix of number of appearance?
Here is another way: xx - data.frame(P = sample(5, 100, TRUE), M = sample(5, 100, TRUE), id = 1:100) require(data.table) xx - data.table(xx) # convert to data.table count - xx[ + , list(count = length(id)) + , by = list(M, P) + ] str(count) Classes ‘data.table’ and 'data.frame': 24 obs. of 3 variables: $ M: int 1 1 1 1 1 2 2 2 2 2 ... $ P: int 1 2 3 4 5 1 2 3 4 5 ... $ count: int 5 4 3 2 9 3 3 6 3 7 ... count M P count 1 1 5 1 2 4 1 3 3 1 4 2 1 5 9 2 1 3 2 2 3 2 3 6 2 4 3 On Mon, Jul 4, 2011 at 5:48 AM, UriB uribl...@gmail.com wrote: I have a matrix of claims at year1 that I get simply by claims-read.csv(file=Claims.csv) qq1-claims[claims$Year==Y1,] I have MemberID and ProviderID for every claim in qq1 both are integers An example for the type of questions that I want to answer is how many times ProviderID number 345 appears together with MemberID 23 in the table qq1 In order to answer these questions for every possible ProviderId and every possible MemberID I would like to have a matrix that has first column as memberID when every memberID in qq1 appears only once and columns that have number of appearance of ProviderID==i for every i that has sum(qq1$ProviderID==i)0 My question is if there is a simple way to do it in R Thanks in Advance Uri -- View this message in context: http://r.789695.n4.nabble.com/How-to-build-a-matrix-of-number-of-appearance-tp3643248p3643248.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. -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] I need help for creating a timevar
Hi Karen, As long as your IDENTITY column goes up in order, this should work: ## example data dat - data.frame(IDENTITY = rep(101:103, 3:1), EVENT = Event) dat$TIMEVAR - unlist(with(dat, tapply(EVENT, IDENTITY, seq_along))) ## Result dat See ?tapply and ?seq_along for some documentation Hope this helps, Josh On Mon, Jul 4, 2011 at 6:41 AM, kbr k...@flicon.de wrote: Hi all! I have data in „Long“ format which I would like to reshape to „Wide“. I know that one possibility is the „reshape“ command, which needs a „timevar“. Data look as follows: There are approx. 3000 persons („IDENTITY“) and, for each person, there are between 2 and 20 events („EVENT“). For now, there's one row for each event (9506 rows) http://r.789695.n4.nabble.com/file/n3643658/Screenshot-2.png What is missing is the „timevar“ (SPSS calls it „INDEX“), which numbers the events WITHIN each person (right column). I managed to number the events from 1 to 9506 with the seq-command, first writing the number of rows in nEVENT: number -seq(file=event, 1, nEVENT, b=1) Yet, I didn't manage to do so for each individual separately. I guess it would be possible with the „split“ command, but I can't figure out how to apply it. Can anyone give me a hint? Thank you! Karen -- View this message in context: http://r.789695.n4.nabble.com/I-need-help-for-creating-a-timevar-tp3643658p3643658.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. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Protecting R code
On Mon, Jul 4, 2011 at 5:48 PM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hey All, Thank you so much for quick replies. Looks like translation to C/C++ is the only robust option. Do you think there exists any ready-made R to C translator? No, I think they are normally all born without the R to C translation skills and acquire them through a long process of going to school and college and spending long long hours studying R and C... I suggest that if your code is so commercially sensitive that you want it written in C, then hire a C programmer to do it. Money well spent. Barry [[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] SOLVED: superimposing different plot types in lattice panel.superpose
Thank you very much Dennis, that's wonderful. I tried it first without LatticeExtra and it didn't work, so yes that package is the key. Best, John -- View this message in context: http://r.789695.n4.nabble.com/superimposing-different-plot-types-in-lattice-panel-superpose-tp3642808p3644145.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] Rpad library
On Jul 4, 2011, at 12:45 PM, ATANU wrote: can anyone help me with a well documented tutorial on Rpad package? I need to do HTML programming in R.Can anyone help me with a tutorial? Trivial Google searching produces this link: http://rpad.googlecode.com/svn-history/r76/Rpad_homepage/index.html -- View this message in context: http://r.789695.n4.nabble.com/Rpad-library-tp3644041p3644041.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Protecting R code
On Mon, Jul 4, 2011 at 2:04 PM, Barry Rowlingson b.rowling...@lancaster.ac.uk wrote: On Mon, Jul 4, 2011 at 5:48 PM, Vaishali Sadaphal vaishali.sadap...@tcs.com wrote: Hey All, Thank you so much for quick replies. Looks like translation to C/C++ is the only robust option. Do you think there exists any ready-made R to C translator? No, I think they are normally all born without the R to C translation skills and acquire them through a long process of going to school and college and spending long long hours studying R and C... I suggest that if your code is so commercially sensitive that you want it written in C, then hire a C programmer to do it. Money well spent. Also -- check out Rcpp: http://cran.r-project.org/web/packages/Rcpp/index.html It will ease some of the R -- C(++) bridging pain, but also provides things like sugar: http://cran.r-project.org/web/packages/Rcpp/vignettes/Rcpp-sugar.pdf Which may make writing your code in C++ a bit easier. YMMV, of course. The library is also GPL though, so I'm not sure what that will make your end code. Although I guess you'll just be linking to it at the end of the day, but I'm not sure what prevailing wisdom these days about whether or not that restricts the license of your code. HTH, -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.
[R] How to merge two files
Dear all, I have two files : seq.txt: NNATTAAAGGGC scores.txt : 0.8 0.7 0.3 0.5 0.6 0.5 0.01 0.9 0.3 0.8 I want output as following A 0.8 T 0.7 T 0.3 A 0.5 A 0.6 A 0.5 G 0.01 G 0.9 G 0.3 C 0.8 Where N are deleted and only A/T/G/C are appearing in a column. Thanks Albert 0.8 0.7 0.3 0.5 0.6 0.5 0.01 0.9 0.3 0.8NNATTAAAGGGC__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] placing multiple rows in a single row
Dear people from the R help list, I have a question that I can't get my head around to start answering, that is why I am writing to the list. I have data in a format like this (tabs might look weird): John A1 1 0 1 John A2 111 John A3 100 MaryA1 1 0 1 Mary A2 001 Mary A3110 Peter A1 100 Peter A2 001 Peter A3 111 Josh A1 1 00 Josh A2 Josh A3000 I want to convert it into a format where variable rows from a single subject are placed behind each other, but with the different scores still matching up (i.e., it needs to be able to cope with missing data, as for Josh's A2 score). John A1 1 0 1 A2 111 A3 100 MaryA1 1 0 1A2 001 A3110 Peter A1 100 A2 001 A3 111 Josh A1 1 00 A2A3000 Preferably, the row identification would become the header of the new table, something like this: A11A12A13 A21A22A23A31A32A33 John 1 0 1 111 100 Mary 1 0 1 001 110 Peter 100 001 111 Josh 1 00 000 Probably, this has been addressed before - I just don't know how to search for the answer with the right search terms. Any help is appreciated, even just a link to a page where this is addressed! Thank you! Annemarie -- Annemarie Verkerk, MA Evolutionary Processes in Language and Culture (PhD student) Max Planck Institute for Psycholinguistics P.O. Box 310, 6500AH Nijmegen, The Netherlands +31 (0)24 3521 185 http://www.mpi.nl/research/research-projects/evolutionary-processes __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] clustering based on most significant pvalues does not separate the groups!
Hi all, I have some microarray data on 40 samples that fall into two groups. I have a value for 480k probes for each of those samples. I performed a t test (rowttests) on each row(giving the indices of the columns for each group) then used p.adjust() to adjust the pvalues for the number of tests performed. I then selected only the probes with adj-p.value=0.05. I end up with roughly 2000 probes to do the clustering on but using pvclust, and hclust, the samples do no split up into the two groups. I would have imagined that using only those values that are significantly different between the two groups, the clustering should surely reflect that? Please, what am I missing??? Thanks! Paul PS: I am hoping I have just thought this through in the wrong way and there is a simple explanation, but can provide the code I am using for clustering if necessary! -- View this message in context: http://r.789695.n4.nabble.com/clustering-based-on-most-significant-pvalues-does-not-separate-the-groups-tp3644249p3644249.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to merge two files
Dear Albert, Here is one way: tmp.scores - readLines(~/scores.txt) tmp.seq - readLines(~/seq.txt) tmp.seq - strsplit(gsub(N, , tmp.seq), )[[1]] genedat - data.frame(Sequence = tmp.seq, Scores = as.numeric(tmp.scores)) ## Yields genedat Sequence Scores 1 A 0.80 2 T 0.70 3 T 0.30 4 A 0.50 5 A 0.60 6 A 0.50 7 G 0.01 8 G 0.90 9 G 0.30 10C 0.80 Hope this helps, Josh 2011/7/4 albert coster albertcoster2...@gmail.com: Dear all, I have two files : seq.txt: NNATTAAAGGGC scores.txt : 0.8 0.7 0.3 0.5 0.6 0.5 0.01 0.9 0.3 0.8 I want output as following A 0.8 T 0.7 T 0.3 A 0.5 A 0.6 A 0.5 G 0.01 G 0.9 G 0.3 C 0.8 Where N are deleted and only A/T/G/C are appearing in a column. Thanks Albert __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology University of California, Los Angeles http://www.joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] placing multiple rows in a single row
On Jul 4, 2011, at 2:32 PM, Annemarie Verkerk wrote: Dear people from the R help list, I have a question that I can't get my head around to start answering, that is why I am writing to the list. I have data in a format like this (tabs might look weird): John A1 1 0 1 John A2 111 John A3 100 MaryA1 1 0 1 Mary A2 001 Mary A3110 Peter A1 100 Peter A2 001 Peter A3 111 Josh A1 1 00 Josh A2 Josh A3000 I want to convert it into a format where variable rows from a single subject are placed behind each other, but with the different scores still matching up (i.e., it needs to be able to cope with missing data, as for Josh's A2 score). John A1 1 0 1 A2 111 A3 1 00 MaryA1 1 0 1A2 001 A31 10 Peter A1 100 A2 001 A3 1 11 Josh A1 1 00 A2A3000 Preferably, the row identification would become the header of the new table, something like this: A11A12A13 A21A22A23A31A32A33 John 1 0 1 111 100 Mary 1 0 1 001 110 Peter 100 001 111 Josh 1 00 000 Probably, this has been addressed before - I just don't know how to search for the answer with the right search terms. Any help is appreciated, even just a link to a page where this is addressed! There is a reshape function in the stats package that nobody except Phil Spector seems to understand and then there is the reshape and reshape2 packages that everybody seems to get. (I don't understand why the classification variables are on the left-hand-side, though. Positionally it makes some sense, but logically it does not connect with how I understand the process.) require(reshape2) # entered your data with default names V1 V2 V3 V4 V5 nam123 V1 V2 V3 V4 V5 1 John A1 1 0 1 2 John A2 1 1 1 3 John A3 1 0 0 4 Mary A1 1 0 1 5 Mary A2 0 0 1 6 Mary A3 1 1 0 7 Peter A1 1 0 0 8 Peter A2 0 0 1 9 Peter A3 1 1 1 10 Josh A1 1 0 0 11 Josh A2 NA NA NA 12 Josh A3 0 0 0 nams.mlt - melt(nam123, idvars=c(V1, V2)) str(nams.mlt) 'data.frame': 36 obs. of 4 variables: $ V1 : Factor w/ 4 levels John,Josh,..: 1 1 1 3 3 3 4 4 4 2 ... $ V2 : Factor w/ 3 levels A1,A2,A3: 1 2 3 1 2 3 1 2 3 1 ... $ variable: Factor w/ 3 levels V3,V4,V5: 1 1 1 1 1 1 1 1 1 1 ... $ value : int 1 1 1 1 0 1 1 0 1 1 ... dcast(nams.mlt, V1+V2 ~ variable) V1 V2 V3 V4 V5 1 John A1 1 0 1 2 John A2 1 1 1 3 John A3 1 0 0 4 Josh A1 1 0 0 5 Josh A2 NA NA NA 6 Josh A3 0 0 0 7 Mary A1 1 0 1 8 Mary A2 0 0 1 9 Mary A3 1 1 0 10 Peter A1 1 0 0 11 Peter A2 0 0 1 12 Peter A3 1 1 1 dcast(nams.mlt, V1 ~ V2+variable) V1 A1_V3 A1_V4 A1_V5 A2_V3 A2_V4 A2_V5 A3_V3 A3_V4 A3_V5 1 John 1 0 1 1 1 1 1 0 0 2 Josh 1 0 0NANANA 0 0 0 3 Mary 1 0 1 0 0 1 1 1 0 4 Peter 1 0 0 0 0 1 1 1 1 You can always change the names of the dataframe if you want, and in this case it would be a simple sub() operation. Personally I would substitute . rather than . -- David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] loop in optim
Hi Edward,
At least for me, your llik() function returns Inf for the starting
values specified, so optim() never gets to estimate anything. You
need to alter llik() or find starting parameters that work before
worrying about getting the for loop working.
Cheers,
Josh
On Mon, Jul 4, 2011 at 2:34 AM, EdBo n.bow...@gmail.com wrote:
Hi
May you help me correct my loop function.
I want optim to estimates al_j; au_j; sigma_j; b_j by looking at 0 to 20,
21 to 40, 41 to 60 data points.
The final result should have 4 columns of each of the estimates AND 4 rows
of each of 0 to 20, 21 to 40, 41 to 60.
###MY code is
n=20
runs=4
out=matrix(0,nrow=runs)
llik = function(x)
{
al_j=x[1]; au_j=x[2]; sigma_j=x[3]; b_j=x[4]
sum(na.rm=T,
ifelse(a$R_j 0, -log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+al_j-b_j*a$R_m))^2,
ifelse(a$R_j0 , -log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+au_j-b_j*a$R_m))^2,
-log(pnorm(au_j,mean=b_j*a$R_m,sd=sqrt(sigma_j^2))-
pnorm(au_j,mean=b_j*a$R_m,sd=sqrt(sigma_j^2)
)
}
start.par = c(0, 0, 0.01, 1)
out1 = optim(llik, par=start.par, method=Nelder-Mead)
for (i in 1: runs)
{
index_start=20*(i-1)+1
index_end= 20*i
out[i]=out1[index_start:index_end]
}
out
Thank you in advance
Edward
UCT
My data
R_j R_m
-0.0625 0.002320654
0 -0.004642807
0.0 0.005936332
0.032258065 0.001060848
0 0.007114057
0.015625 0.005581558
0 0.002974794
0.015384615 0.004215271
0.060606061 0.005073116
0.028571429 -0.006001279
0 -0.002789594
0.01389 0.00770633
0 0.000371663
0.02739726 -0.004224228
-0.04 0.008362539
0 -0.010951605
0 0.004682924
0.01389 0.011839993
-0.01369863 0.004210383
-0.02778 -0.04658949
0 0.00987272
-0.057142857 -0.062203157
-0.03030303 -0.119177639
0.09375 0.077054642
0 -0.022763619
-0.057142857 0.050408775
0 0.024706076
-0.03030303 0.004043701
0.0625 0.004951088
0 -0.005968731
0 -0.038292548
0 0.013381097
0.014705882 0.006424728
-0.014492754 -0.020115626
0 -0.004837891
-0.029411765 -0.022054654
0.03030303 0.008936428
0.044117647 8.16925E-05
0 -0.004827246
-0.042253521 0.004653096
-0.014705882 -0.004222151
0.029850746 0.000107267
-0.028985507 -0.001783206
0.029850746 -0.006372981
0.014492754 0.005492374
-0.028571429 -0.009005846
0 0.001031683
0.044117647 0.002800551
--
View this message in context:
http://r.789695.n4.nabble.com/loop-in-optim-tp3643230p3643230.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.
--
Joshua Wiley
Ph.D. Student, Health Psychology
University of California, Los Angeles
http://www.joshuawiley.com/
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] R CMD SHLIB with ifort
Hi, I am running Linux (64 bit) R, compiled under gnu compilers. I am looking to compile a Fortran program with the ifort (the intel compiler) and then be able to import that as a library into my version of R. I am using the flags FC=ifort and SHLIB_FCLD=ifort, however ifort does not seem to recognize the libR.so file. Does any one have experience with this/know of a a way to load an ifort compiled file into R. Thanks! --- Ted Rosenbaum Graduate Student Yale University Department of Economics [[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] R CMD SHLIB with ifort
I don't have any idea about linking Fortran to R, but if I did I am sure I would want complete command lines and error messages before I looked at your problem. --- Jeff Newmiller The . . Go Live... DCN:jdnew...@dcn.davis.ca.us Basics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/Batteries O.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. Ted Rosenbaum rosen...@gmail.com wrote: Hi, I am running Linux (64 bit) R, compiled under gnu compilers. I am looking to compile a Fortran program with the ifort (the intel compiler) and then be able to import that as a library into my version of R. I am using the flags FC=ifort and SHLIB_FCLD=ifort, however ifort does not seem to recognize the libR.so file. Does any one have experience with this/know of a a way to load an ifort compiled file into R. Thanks! _ Ted Rosenbaum Graduate Student Yale University Department of Economics [[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] modification of cross-validations in rpart
One way around hacking rpart is to write code to do K fold samples based on unit outside rpart, then build trees using training sets and summarize scores on testing sets. Weidong Gu On Mon, Jul 4, 2011 at 9:22 AM, Katerine Goyer katerine.go...@uqtr.ca wrote: Hello, I am using the rpart function (from the rpart package) to do a regression tree that would describe the behaviour of a fish species according to several environmental variables. For each fish (sampling unit), I have repeated observations of the response variable, which means that the data are not independent. Normally, in this case, V-fold cross-validation needs to be modified to prevent over-optimistic predictions of error rates by cross-validation and overestimation of the tree size. A way to overcome this problem is by selecting only whole sampling units in our subsets of cross-validation. My problem is that I don’t know how to perform this modification of the cross-validation process in the rpart function. Is there a way to do this modification in rpart or is there any other function I could use that would consider interdependence in the response variable? Here is an example of the code I am using (“Y” being the response variable and “data.env” being a data frame of the environmental variables): Tree = rpart(Y ~ X1 + X2 + X3,xval=100,data=data.env) Thanks Katerine [[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] FinCenter in timeSeries with merge, cbind and rbind
Hi R users: When I try to merge or bind (cbind or rbind) two series, both with a FinCenter different that GMT, the result is GMT not the original financial center? What am I doing wrong? ## require(timeSeries) getRmetricsOptions(myFinCenter) setRmetricsOptions(myFinCenter = America/Bogota) getRmetricsOptions(myFinCenter) fechas - format(timeCalendar(2010, sample(12, 6))) datos - matrix(round(rnorm(6), 3)) t1 - sort(timeSeries(datos, fechas, units = A)) t1 fechas - format(timeCalendar(2010, sample(12, 6))) datos - matrix(round(rnorm(6), 3)) t2 - sort(timeSeries(datos, fechas, units = B)) t2 merge(t1,t2) cbind(t1,t2) rbind(t1,t2) ## Thank you for your help. Kenneth __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Low Pain Unicode Characters in pdf graph?
On Sun, May 15, 2011 at 3:06 PM, ivo welch ivo.we...@gmail.com wrote: Dear R-experts---is there a relatively low-pain way to get unicode characters into a plot to a pdf device? Have you tried Cairo package or cairo_pdf()? Both are making use of Cairo, which uses UTF-8 and automatically embeds fonts. Regards Liviu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Stuck ...can't get sapply and xmlTreeParse working
Can't seem to get the code below working. It gets stuck on line 24 inside the
function hm; comments show the line in question. The function hm is called
by sapply and is at the bottom of the code. Other stuff above line 24 works
correctly including the first couple of lines of the function hm. Should I
be using a different apply function or am I doing something wrong with
xmlTreeParse ?
library(XML)
url.montco -
http://webapp.montcopa.org/sherreal/salelist.asp?saledate=07/27/2011;
tbl -data.frame(readHTMLTable(url.montco))[, c(3,5,6,8,9)]
tbl -tbl[2: length(tbl[,1]),]
names(tbl) - c(Address, Township, Parcel, SaleDate, Costs);
rownames(tbl) - NULL
v - gregexpr(( aka )|( AKA ),tbl$Address)
s -sapply(v, function(x) max(unlist(x)))
tbl$Address - substring(tbl$Address, ifelse(s== -1, 0, s+4), 1)
tbl$Cost - gsub(',', '', tbl$Costs)
temp - strsplit(tbl$Cost, \\$)
temp - do.call(rbind, temp) # create a matrix
mode(temp) - 'numeric'
tbl$Debt - round(temp[, 2]/1000,2)
tbl$Court - round(temp[, 3]/1000,2)
z - data.frame(substr(tbl$SaleDate,regexpr([A-Za-z], tbl$SaleDate),
regexpr([0-9], tbl$SaleDate,)-1)) ; names(z) - Action
y - data.frame(substr(tbl$SaleDate,regexpr([0-9], tbl$SaleDate),2011)) ;
names(y) - ActionDate
tbl -cbind(tbl[, c(1,2,3,7,8)],z,y)
new.add - paste(tbl$Address,citystatezip=,tbl$Township,%2C+PA, sep='')
new.add - sub(^( )+,, new.add)
new.add -data.frame(gsub(( )+,'+', new.add)); names(new.add) -
ParseAddress
hm - function(x) {
url.zill
-paste(http://www.zillow.com/webservice/GetDeepSearchResults.htm?zws-id=X1-ZWz1bup03e49vv_5kvb6address=,x,
sep=)
## problem line is next #
zdoc -xmlTreeParse(url.zill, useInternalNode=TRUE, isURL=TRUE)
# problem line above ##
f$zpid - sapply(getNodeSet(zdoc, //result/zpid), xmlValue)
f$zest.low -sapply(getNodeSet(zdoc, //valuationRange/low), xmlValue)
f$zest - sapply(getNodeSet(zdoc, //zestimate/amount), xmlValue)
rm(zdoc)
return(f)
}
j -sapply(new.add, FUN=hm)
print(zest)
--
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Re: [R] [R-SIG-Finance] FinCenter in timeSeries with merge, cbind and rbind
On Jul 4, 2011, at 6:47 PM, Kenneth Roy Cabrera Torres wrote: Hi R users: When I try to merge or bind (cbind or rbind) two series, both with a FinCenter different that GMT, the result is GMT not the original financial center? It's not in the help(cbind.timeSeries) page but looking at the function (and at the documentation for the timeSeries class) you see that there is a zone argument and that it is GMT by default. So why don't you add something meaningful to your code (... that is not presented in a reproducible manner for testing.) It is listed in the documentation as zone=, but in the cbind function call, the code is zone=GMT. It appears that the zone argument might be for input and the FinCenter might be for output in the help page for timeDate, but I think that aspect of the various parts of the documentation is rather vague and might do with a bit of clarification. -- David. What am I doing wrong? ## require(timeSeries) getRmetricsOptions(myFinCenter) setRmetricsOptions(myFinCenter = America/Bogota) getRmetricsOptions(myFinCenter) fechas - format(timeCalendar(2010, sample(12, 6))) datos - matrix(round(rnorm(6), 3)) t1 - sort(timeSeries(datos, fechas, units = A)) t1 fechas - format(timeCalendar(2010, sample(12, 6))) datos - matrix(round(rnorm(6), 3)) t2 - sort(timeSeries(datos, fechas, units = B)) t2 merge(t1,t2) cbind(t1,t2) rbind(t1,t2) ## Thank you for your help. Kenneth ___ r-sig-fina...@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-sig-finance -- Subscriber-posting only. If you want to post, subscribe first. -- Also note that this is not the r-help list where general R questions should go. ___ e at 1 Churchill Place, London, E14 5HP. This email may relate to or be sent from other members of the Barclays Group. ___ __ This email has been scanned by the MessageLabs Email Security System. For more information please visit http://www.messagelabs.com/email __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Seasonality of time series
Dear all, I have a time series of 10-day tropical rainfall data with a typical rainy and dry season. Is there a way to extract seasonal information with R, like the day of the start and end of each rainy season for each year? Martin Brandt University of Vienna -- View this message in context: http://r.789695.n4.nabble.com/Seasonality-of-time-series-tp3644985p3644985.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] Bad Confirmation String
I just signed up for R-help 2 days ago, and received an *Invalid confirmation string:*2beb5b0883f29fae71a80fcb30324117ec9ece94 when confirming subscription. I am receiving e-mails in my inbox with about 40% of individual e-mails saying across the top this message may not have been sent by: n...@somee-mail.com. Is this cause for concern? Should these messages be reported as phishing, and should I mark messages received in my inbox with the message this message may not have been sent by. . . as spam? -- Matilda Gogos matildaelizabe...@gmail.com [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Stuck ...can't get sapply and xmlTreeParse working
The value of 'url.zill' is a vector of 407 character strings:
Browse[1] str(url.zill)
chr [1:407]
http://www.zillow.com/webservice/GetDeepSearchResults.htm?zws-id=X1-ZWz1bup03e49vv_5kvb6address=10+PACER+LNcitystatezip=East+;|
__truncated__ ...
Isn't it supposed to be just a single file name?
On Mon, Jul 4, 2011 at 8:42 PM, eric ericst...@aol.com wrote:
Can't seem to get the code below working. It gets stuck on line 24 inside the
function hm; comments show the line in question. The function hm is called
by sapply and is at the bottom of the code. Other stuff above line 24 works
correctly including the first couple of lines of the function hm. Should I
be using a different apply function or am I doing something wrong with
xmlTreeParse ?
library(XML)
url.montco -
http://webapp.montcopa.org/sherreal/salelist.asp?saledate=07/27/2011;
tbl -data.frame(readHTMLTable(url.montco))[, c(3,5,6,8,9)]
tbl -tbl[2: length(tbl[,1]),]
names(tbl) - c(Address, Township, Parcel, SaleDate, Costs);
rownames(tbl) - NULL
v - gregexpr(( aka )|( AKA ),tbl$Address)
s -sapply(v, function(x) max(unlist(x)))
tbl$Address - substring(tbl$Address, ifelse(s== -1, 0, s+4), 1)
tbl$Cost - gsub(',', '', tbl$Costs)
temp - strsplit(tbl$Cost, \\$)
temp - do.call(rbind, temp) # create a matrix
mode(temp) - 'numeric'
tbl$Debt - round(temp[, 2]/1000,2)
tbl$Court - round(temp[, 3]/1000,2)
z - data.frame(substr(tbl$SaleDate,regexpr([A-Za-z], tbl$SaleDate),
regexpr([0-9], tbl$SaleDate,)-1)) ; names(z) - Action
y - data.frame(substr(tbl$SaleDate,regexpr([0-9], tbl$SaleDate),2011)) ;
names(y) - ActionDate
tbl -cbind(tbl[, c(1,2,3,7,8)],z,y)
new.add - paste(tbl$Address,citystatezip=,tbl$Township,%2C+PA, sep='')
new.add - sub(^( )+,, new.add)
new.add -data.frame(gsub(( )+,'+', new.add)); names(new.add) -
ParseAddress
hm - function(x) {
url.zill
-paste(http://www.zillow.com/webservice/GetDeepSearchResults.htm?zws-id=X1-ZWz1bup03e49vv_5kvb6address=,x,
sep=)
## problem line is next #
zdoc -xmlTreeParse(url.zill, useInternalNode=TRUE, isURL=TRUE)
# problem line above ##
f$zpid - sapply(getNodeSet(zdoc, //result/zpid), xmlValue)
f$zest.low -sapply(getNodeSet(zdoc, //valuationRange/low), xmlValue)
f$zest - sapply(getNodeSet(zdoc, //zestimate/amount), xmlValue)
rm(zdoc)
return(f)
}
j -sapply(new.add, FUN=hm)
print(zest)
--
View this message in context:
http://r.789695.n4.nabble.com/Stuck-can-t-get-sapply-and-xmlTreeParse-working-tp3644894p3644894.html
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__
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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.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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[R] Fw: volcano plot.r
Hello.
My name is Akashah. i work at metabolic laboratory. From my study, i found that
volcano plot can help a lot in my section.
i already studied about the volcano plot and get the coding to run in R
software, unfortunately, there is may be something wrong with the coding. This
is because no graph appear, but no error (blue color text) was shown on the R
console. Below is the coding for volcano plot, i hope anybody can help me to
solve the problem.
# volcano_plot.r
#
# Author: Amsha Nahid, Jairus Bowne, Gerard Murray
# Purpose: Produces a volcano plot
#
# Input: Data matrix as specified in Data-matrix-format.pdf
# Output: Plots log2(fold change) vs log10(t-test P-value)
#
# Notes: Group value for control must be alphanumerically first
# Script will return an error if there are more than 2 groups
#
# Load the data matrix
#
# Read in the .csv file
data-read.csv(file:///Users/nadya/Desktop/praktikal UTM/TASKS1/RT BE EMS
300-399.csv, sep=,, row.names=1, header=TRUE)
# Get groups information
groups-data[,1]
# Get levels for groups
grp_levs-levels(groups)
if (length(levels(groups)) 2)
print(Number of groups is greater than 2!) else {
#
# Split the matrix by group
#
new_mats-c()
for (ii in 1:length(grp_levs))
new_mats[ii]-list(data[which(groups==levels(groups)[ii]),])
#
# Calculate the means
#
# For each matrix, calculate the averages per column
submeans-c()
# Preallocate a matrix for the means
means-matrix(
nrow = 2,
ncol = length(colnames(data[,-1])),
dimnames = list(grp_levs,colnames(data[,-1]))
)
# Calculate the means for each variable per sample
for (ii in 1:length(new_mats))
{submeans[ii]-list(apply(new_mats[[ii]][,-1],2,mean,na.rm=TRUE))
means[ii,]-submeans[[ii]]}
#
# Calculate the fold change
#
folds-matrix(
nrow=length(means[,1]),
ncol=length(means[1,]),
dimnames=list(rownames(means),colnames(means))
)
for (ii in 1:length(means[,1]))
for (jj in 1:length(means[1,]))
folds[ii,jj]-means[ii,jj]/means[1,jj]
#
# t-test P value data
#
pvals-matrix(nrow=ncol(data[,-1]),ncol=1,dimnames=list(colnames(data[-1]),P-Value))
#
# Perform the t-Test
#
for(ii in 1:nrow(pvals)) {
pvals[ii,1]-t.test(new_mats[[1]][,ii+1],new_mats[[2]][,ii+1])$p.value
}
m-length(pvals)
x_range-range(c(
min(
range(log2(folds[2,])),
range(c(-1.5,1.5))
),
max(
range(log2(folds[2,])),
range(c(-1.5,1.5))
)
))
y_range-range(c(
min(range(-log10(pvals)),
range(c(0,2))
),
max(range(-log10(pvals)),
range(c(0,2))
)
))
#
# Plot data
#
# Define a function, since it's rather involved
volcano_plot-function(fold, pval)
{plot(x_range, # x-dim
y_range, # y-dim
type=n, # empty plot
xlab=log2 Fold Change, # x-axis title
ylab=-log10 t-Test P-value, # y-axis title
main=Volcano Plot, # plot title
)
abline(h=-log10(0.05),col=green,lty=44)# horizontal line at
P=0.05
abline(v=c(-1,1),col=violet,lty=1343) # vertical lines at
2-fold
# Plot points based on their values:
for (ii in 1:m)
# If it's below 0.05, we're not overly interested: purple.
if (-log10(pvals[ii])(-log10(0.05))) {
# Otherwise, more checks;
# if it's greater than 2-fold decrease: blue
if (log2(folds[2,][ii])(-1)) {
# If it's significant but didn't change much: orange
if (log2(folds[2,][ii])1) {
points(
log2(folds[2,][ii]),
-log10(pvals[ii]),
col=orange,
pch=20
)
# Otherwise, greater than 2-fold increase: red
} else {
points(
log2(folds[2,][ii]),
-log10(pvals[ii]),
col=red,
pch=20
)
}
} else {
points(
log2(folds[2,][ii]),
-log10(pvals[ii]),
Re: [R] Stuck ...can't get sapply and xmlTreeParse working
Probably this is what you want; convert the first column of 'new.add'
to character and then use in the sapply.
Now it seems to work in that data is read in, but the new error is
that f is not defined. What is it supposed to be?
x - as.character(new.add[[1]])
z - sapply(x, hm)
Error in f$zpid - sapply(getNodeSet(zdoc, //result/zpid), xmlValue) :
object 'f' not found
Enter a frame number, or 0 to exit
1: sapply(x, hm)
2: lapply(X, FUN, ...)
3: FUN(c(10+PACER+LNcitystatezip=East+Norriton%2C+PA,
141+ROSEMONT+AVEcitystatezip=Norristown%2C+PA, 6
On Mon, Jul 4, 2011 at 8:42 PM, eric ericst...@aol.com wrote:
Can't seem to get the code below working. It gets stuck on line 24 inside the
function hm; comments show the line in question. The function hm is called
by sapply and is at the bottom of the code. Other stuff above line 24 works
correctly including the first couple of lines of the function hm. Should I
be using a different apply function or am I doing something wrong with
xmlTreeParse ?
library(XML)
url.montco -
http://webapp.montcopa.org/sherreal/salelist.asp?saledate=07/27/2011;
tbl -data.frame(readHTMLTable(url.montco))[, c(3,5,6,8,9)]
tbl -tbl[2: length(tbl[,1]),]
names(tbl) - c(Address, Township, Parcel, SaleDate, Costs);
rownames(tbl) - NULL
v - gregexpr(( aka )|( AKA ),tbl$Address)
s -sapply(v, function(x) max(unlist(x)))
tbl$Address - substring(tbl$Address, ifelse(s== -1, 0, s+4), 1)
tbl$Cost - gsub(',', '', tbl$Costs)
temp - strsplit(tbl$Cost, \\$)
temp - do.call(rbind, temp) # create a matrix
mode(temp) - 'numeric'
tbl$Debt - round(temp[, 2]/1000,2)
tbl$Court - round(temp[, 3]/1000,2)
z - data.frame(substr(tbl$SaleDate,regexpr([A-Za-z], tbl$SaleDate),
regexpr([0-9], tbl$SaleDate,)-1)) ; names(z) - Action
y - data.frame(substr(tbl$SaleDate,regexpr([0-9], tbl$SaleDate),2011)) ;
names(y) - ActionDate
tbl -cbind(tbl[, c(1,2,3,7,8)],z,y)
new.add - paste(tbl$Address,citystatezip=,tbl$Township,%2C+PA, sep='')
new.add - sub(^( )+,, new.add)
new.add -data.frame(gsub(( )+,'+', new.add)); names(new.add) -
ParseAddress
hm - function(x) {
url.zill
-paste(http://www.zillow.com/webservice/GetDeepSearchResults.htm?zws-id=X1-ZWz1bup03e49vv_5kvb6address=,x,
sep=)
## problem line is next #
zdoc -xmlTreeParse(url.zill, useInternalNode=TRUE, isURL=TRUE)
# problem line above ##
f$zpid - sapply(getNodeSet(zdoc, //result/zpid), xmlValue)
f$zest.low -sapply(getNodeSet(zdoc, //valuationRange/low), xmlValue)
f$zest - sapply(getNodeSet(zdoc, //zestimate/amount), xmlValue)
rm(zdoc)
return(f)
}
j -sapply(new.add, FUN=hm)
print(zest)
--
View this message in context:
http://r.789695.n4.nabble.com/Stuck-can-t-get-sapply-and-xmlTreeParse-working-tp3644894p3644894.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.
--
Jim Holtman
Data Munger Guru
What is the problem that you are trying to solve?
__
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Protecting R code
On 11-07-04 3:47 AM, Vaishali Sadaphal wrote: Hi All, I need to give my R code to my client to use. I would like to protect the logic/algorithms that have been coded in R. This means that I would not like anyone to be able to read the code. R is an open source project, so providing ways for you to do this is not one of our goals. If I were your client I would have asked for the source code for whatever you're doing; if your client isn't savvy enough to do that, you should provide it and explain why it is useful, and what your client is and isn't allowed to do with it. If you think your client will steal from you, then you should find another client. Duncan Murdoch I am searching for ways to protect R code. I would like to create a .exe kind of file which could be executed without using R or requiring to install R. I would not like the R code to be loaded in R. This is so because, after R loads a function, if you type the function name on the command prompt, you can see the complete code. I would not like to give this type of access to the R code. I explored the option of creating .bat file (using command: R CMD BAT) and byte code (using command: compile). These are not useful since they open R, load these functions and then the R code is visible. Is there any other way to protect the R code which would help me package all my files/source files and give me an executable file which would be run without opening R? Another problem is that R is freely downloadable. Is it somehow possible to protect the code from being loaded in R and being seen. Thanks -- Vaishali =-=-= Notice: The information contained in this e-mail message and/or attachments to it may contain confidential or privileged information. If you are not the intended recipient, any dissemination, use, review, distribution, printing or copying of the information contained in this e-mail message and/or attachments to it are strictly prohibited. If you have received this communication in error, please notify us by reply e-mail or telephone and immediately and permanently delete the message and any attachments. Thank you [[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] loop in optim
Hi
I have re-worked on my likelihood function and it is now working(#the code
is below#).
May you help me correct my loop function.
I want optim to estimates al_j; au_j; sigma_j; b_j by looking at 0 to 20,
21 to 40, 41 to 60 data points.
The final result should have 4 columns of each of the estimates AND 4 rows
of each of 0 to 20, 21 to 40, 41 to 60.
#likelihood function
a=read.table(D:/hope.txt,header=T)
attach(a)
a
llik = function(x)
{
al_j=x[1]; au_j=x[2]; sigma_j=x[3]; b_j=x[4]
sum(na.rm=T,
ifelse(a$R_j 0, log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+al_j-b_j*a$R_m))^2,
ifelse(a$R_j0 , log(1/(2*pi*(sigma_j^2)))-
(1/(2*(sigma_j^2))*(a$R_j+au_j-b_j*a$R_m))^2,
log(ifelse (( pnorm (au_j, mean=b_j * a$R_m,
sd= sqrt(sigma_j^2))-
pnorm(al_j, mean=b_j * a$R_m, sd=sqrt (sigma_j^2)
)) 0,
(pnorm (au_j,mean=b_j * a$R_m, sd=
sqrt(sigma_j^2))-
pnorm(al_j, mean=b_j * a$R_m, sd= sqrt(sigma_j^2)
)),
1)) ))
)
}
start.par = c(-0.01,0.01,0.1,1)
out1 = optim(llik, par=start.par, method=Nelder-Mead)
out1
--
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Create factor variable by groups
Hi, suppose that I have the following data.frame: cnae4 cnpj 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 Y 24996 10020470 1 1 2 12 16 21 17 51 43 19 183 24996 10020470 69 91 79 92 91 77 90 96 98 108 891 36145 10020470 0 0 0 0 2 83 112 97 91 144 529 4 1002 5 20 60 0 0 0 0 5 20 1000 1110 I would like to create a new variable X that indicates which line, within the cnpj variable, has the highest value Y. For instance, within the cnpj = 10020470, the second line has the largest value Y (891). For cnpj = 1002 is trivial (1110). Then, my new data.frame would become: cnae4 cnpj 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 Y X 24996 10020470 1 1 2 12 16 21 17 51 43 19 183 FALSE 24996 10020470 69 91 79 92 91 77 90 96 98 108 891 TRUE 36145 10020470 0 0 0 0 2 83 112 97 91 144 529 FALSE 4 1002 5 20 60 0 0 0 0 5 20 1000 1110 TRUE Notice that for every value of the variable cnpj, only one line will have X = TRUE. Then, I would like to create a variable Z that is the sum of variable Y, also by variable cnpj. Thus, if cnpj = 10020470, Z = 183 + 891 +529 and for cnpj = 1002, Z = 120. These sums can easily be done with tapply or aggregate but those would eliminate line with equal cnpj and I donât want that. I would like to achieve a data.frame like the following: cnae4 cnpj 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 Y X Z 24996 10020470 1 1 2 12 16 21 17 51 43 19 183 FALSE 1603 24996 10020470 69 91 79 92 91 77 90 96 98 108 891 TRUE 1603 36145 10020470 0 0 0 0 2 83 112 97 91 144 529 FALSE 1603 4 1002 5 20 60 0 0 0 0 5 20 1000 1110 TRUE 1110 In the end I will eliminate all lines with X = FALSE. Thank you and sorry for the long question. Mateus Rabello [[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] Prevent 'R CMD check' from reporting NA/NA_character_ missmatch?
Prof Brian Ripley wrote: On Mon, 4 Jul 2011, Johannes Graumann wrote: Hello, I'm writing a package am running 'R CMD check' on it. Is there any way to make 'R CMD check' not warn about a missmatch between 'NA_character_' (in the function definition) and 'NA' (in the documentation)? Be consistent Why do you want incorrect documentation of your package? (It is not clear of the circumstances here: normally 1 vs 1L and similar are not reported if they are the only errors.) And please do note the posting guide - this is not really the correct list - you were asked to give an actual example with output. Taken to R-devel. Thanks. Joh __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
