Re: [R] Creating ODS RTF-style output in R XXXX
Dan Abner wrote: I have been using the sink() function as follows: x-rnorm(100) sink(C:\\Users\\dan\\Desktop\\Current Events\\myhw.txt, append=TRUE,split=TRUE) m1-c(Mean=mean(x),SD=sd(x),Min=min(x),Max=max(x)) m1 sink() === Is it possible to create tabular style output very much like the ODS RTF STYLE=JOURNAL protocol in SAS (which returns a nicely formatted table with table lines and easily opened in MS Word)? Not with sink, but odfWeave can do this, but it's a bit more work initially. Dieter -- View this message in context: http://r.789695.n4.nabble.com/Creating-ODS-RTF-style-output-in-R--tp314p3778018.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 do I get a weighted frequency table?
Thank you, that's works just fine. Luca Il giorno 29/ago/2011, alle ore 23.48, H. T. Reynolds ha scritto: Hi, I use xtabs with the weight variable on the left hand side of the formula as in xtabs(weight ~ opinion + gender + ...) __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Saving a graph
On Mon, 29 Aug 2011, Dieter Menne wrote: Gang Chen-4 wrote: However, my problem is that the file generated from a graph of fixed size is too large (in the order of 10MB) because of many data points in multiple scatterplots. Any suggestions? Generate pdf, open and save it in Adobe Acrobat which does a compression when the setting are correct. *If* compression is enough, pdf() in R-devel does it, as does cairo_pdf() in current R. And there are other ways than Acrobat to compress/compact a PDF file: see ?tools::compactPDF and the 'Writing R Extensions' manual. However, compression will not make that much of a difference (maybe a factor of 3), and the real problem seems to be the inappropriate plot. If you really need a plot with hundreds of thousands of points (or more), use a format like PNG -- but there are better ways to display such plots for most statistical purposes. E.g. image and contour plots of densities, hexplots, density-dependent thinning -- 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] Ordinal logistic regression p-values
There is also clm() (for cumulative link models) from package ordinal that has much the same interface that polr() has, but it does give you p-values for the regression parameters. A simple example from examples(clm): library(ordinal) data(wine) fm1 - clm(rating ~ contact + temp, data=wine) (summ - summary(fm1)) giving the output: formula: rating ~ contact + temp data:wine link threshold nobs logLik AICniter max.grad cond.H logit flexible 72 -86.49 184.98 6(0) 4.01e-12 2.7e+01 Coefficients: Estimate Std. Error z value Pr(|z|) contactyes 1.5278 0.4766 3.205 0.00135 ** tempwarm 2.5031 0.5287 4.735 2.19e-06 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 Threshold coefficients: Estimate Std. Error z value 1|2 -1.3444 0.5171 -2.600 2|3 1.2508 0.4379 2.857 3|4 3.4669 0.5978 5.800 4|5 5.0064 0.7309 6.850 The p-values are extracted with: coef(summ)[5:6, 4] contactyes tempwarm 1.348440e-03 2.194605e-06 Cheers, Rune On 30 August 2011 03:30, Frank Harrell f.harr...@vanderbilt.edu wrote: Use the rms package to replace Design. Run anova(fit object from lrm) which produces a matrix from which you can extract P-values. This also handles the case of multiple degrees of freedom per predictor. Frank Debs Majumdar wrote: Hi, Are there any packages which prints out p-values for OLR's (like `ologit' from Stata)? I want to run a bunch of OLRs and print the p-value for the first coefficient from each of them. I checked polr() under MASS and it doesn't. There's a lrm() function under Design which does print out p-values but I couldn't extract p-values from the output. Thanks, Debs __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. - Frank Harrell Department of Biostatistics, Vanderbilt University -- View this message in context: http://r.789695.n4.nabble.com/Ordinal-logistic-regression-p-values-tp3777674p368.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. -- Rune Haubo Bojesen Christensen Ph.D. Student, M.Sc. Eng. Phone: (+45) 45 25 33 63 Mobile: (+45) 30 26 45 54 DTU Informatics, Section for Statistics Technical University of Denmark, Build. 305, Room 122, DK-2800 Kgs. Lyngby, Denmark __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Differences in SAS and R defaults
Yes, something similar would be helpful but not among SAS proc but between SAS and R. Thanks Nikhil On Mon, Aug 29, 2011 at 11:08 PM, Jeremy Miles jeremy.mi...@gmail.comwrote: Do you mean things like treatment of categorical variables in regression procedures (which have different defaults in different procedures in SAS), and different default as to the reference category in logistic regression? Jeremy On 29 August 2011 04:46, n nikhil.abhyan...@gmail.com wrote: Hello all, I am looking for theories and statistical analyses where the defaults employed in R and SAS are different. As a result, the outputs under the defaults should (at least slightly) differ for the same input. Could anyone kindly point any such instance? Thanks Nikhil __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Conditional plots in the soiltexture package
Dear Alessandro I am not sure what you mean by conditional plot But if it is about having a different symbol, for different soil parent materials, you can use the pch argument in TT.plot() ### require( soiltexture ) # :: 1st create a dummy texture dataset my.text - data.frame( CLAY = c(05,60,15,05,25,05,25,45,65,75,13,47), SILT = c(05,08,15,25,55,85,65,45,15,15,17,43), SAND = c(90,32,70,70,20,10,10,10,20,10,70,10), parent= rep(1:2,each=6) # parent material and symbol code ) # dim( my.text ) TT.plot( tri.data = my.text, pch = my.text[,parent] ) ### Is that what you need? All the best Julien From: r-help-boun...@r-project.org [r-help-boun...@r-project.org] On Behalf Of samuel-rosa [alessandrosam...@yahoo.com.br] Sent: 30 August 2011 03:48 To: r-help@r-project.org Subject: [R] Conditional plots in the soiltexture package Dear R users I'd like to know if it is possible to create conditional plots in the soiltexture package. I have data from the particle size distribution of soils derived from two parent materials and I want to use the parent material as conditioner. Thanks a lot. Alessandro Samuel-Rosa Post-Graduation Program in Soil Science Federal University of Santa Maria Av. Roraima, nº 1000, CEP 97105-970 Santa Maria, RS, Brazil -- View this message in context: http://r.789695.n4.nabble.com/Conditional-plots-in-the-soiltexture-package-tp383p383.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R-Studio Question
Hello, I've switched to R studio from the StatET Eclipse plug-in. I have a question regarding navigating between plots. When I use x11() or windows() new devices are created and I know how to switch back and forth between them. However, when I plot on the device that stands for R-Studio's built-in plot browser, is there a way to switch back between plots? Each new plot command opens a new plot, and the number of devices does not change. Thanks, Eran. [[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] Showing zero frequencies with xtabs
Hi, Does anyone know how to show zero frequencies variable levels with the xtabs command? They show with the table(x,y) command but I need to apply weight to frequency tables and I also need to cbind several tables together, which implies that they all need to show the same number of rows. Alternatively, do you know how to column bind tables with different number of rows? I cannot use merge as it requires daata.frame and that modifies the look of the banner table I am trying to create... Thanks, Luca Mr. Luca Meyer www.lucameyer.com R version 2.13.1 (2011-07-08) Mac OS X 10.6.8 [[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] Showing zero frequencies with xtabs
On Aug 30, 2011, at 10:04 , Luca Meyer wrote: Hi, Does anyone know how to show zero frequencies variable levels with the xtabs command? They show with the table(x,y) command but I need to apply weight to frequency tables and I also need to cbind several tables together, which implies that they all need to show the same number of rows. Are you sure you are doing the same thing as with table(). I'd expect it to work if you ensure that the variables are factors: library(ISwR) xtabs(~sex+menarche,data=juul) menarche sex 1 2 2 369 335 juul$sex - factor(juul$sex,levels=1:2) xtabs(~sex+menarche,data=juul) menarche sex 1 2 1 0 0 2 369 335 Alternatively, do you know how to column bind tables with different number of rows? I cannot use merge as it requires daata.frame and that modifies the look of the banner table I am trying to create... Thanks, Luca Mr. Luca Meyer www.lucameyer.com R version 2.13.1 (2011-07-08) Mac OS X 10.6.8 [[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. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Showing zero frequencies with xtabs
Hi Hi, Does anyone know how to show zero frequencies variable levels with the xtabs command? They show with the table(x,y) command but I need to apply weight to frequency tables and I also need to cbind several tables together, which implies that they all need to show the same number of rows. Do you use factors? x-sample(letters[1:5], 20, replace=T) xtabs(~x) x a b c d e 2 1 5 4 8 x.f-factor(x) x[x==b]-NA x.f[x.f==b]-NA xtabs(~x) x a c d e 2 5 4 8 xtabs(~x.f) x.f a b c d e 2 0 5 4 8 With factors you can specify also non existent levels so they shall appear as zeroes in table or xtabs. Regards Petr Alternatively, do you know how to column bind tables with different number of rows? I cannot use merge as it requires daata.frame and that modifies the look of the banner table I am trying to create... Thanks, Luca Mr. Luca Meyer www.lucameyer.com R version 2.13.1 (2011-07-08) Mac OS X 10.6.8 [[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] Configuring Proxy: Proxy Authentication Required with --internet2
That was my first guess as well, but unfortunately this doesn't solve the problem. I is remarkably that IE requires authentification for every new instance I open (even if another instance is already open)... Any other hints? -- View this message in context: http://r.789695.n4.nabble.com/Configuring-Proxy-Proxy-Authentication-Required-with-internet2-tp3776209p3778151.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] ARMA show different result between eview and R
When I do ARMA(2,2) using one lag of LCPIH data This is eview result *Dependent Variable: DLCPIH **Method: Least Squares **Date: 08/12/11 Time: 12:44 **Sample (adjusted): 1970Q2 2010Q2 **Included observations: 161 after adjustments **Convergence achieved after 14 iterations **MA Backcast: 1969Q4 1970Q1 ** **VariableCoefficientStd. Errort-StatisticProb. ** **C0.0033610.0018141.8533520.0657 **DLCPIH(-1)-0.1001500.053160-1.8839170.0614 **DLCPIH(-2)0.8704560.05246616.590750. **MA(1)0.5322520.1001105.3166780. **MA(2)-0.3793830.099535-3.8115660.0002 ** **R-squared0.512067Mean dependent var0.014816 **Adjusted R-squared0.499556S.D. dependent var0.016274 **S.E. of regression0.011513Akaike info criterion -6.060182 **Sum squared resid0.020676Schwarz criterion-5.964486 **Log likelihood492.8446Hannan-Quinn criter.-6.021326 **F-statistic40.92897Durbin-Watson stat2.012062 **Prob(F-statistic)0.00 ** **Inverted MA Roots .40 -.94 * This is R result * dlcpihTsLen - length(ausT2Ts[,4]) ** dlcpihArma22Fit - arima(ausT2Ts[,4], order=c(2,1,2), xreg=1:dlcpihTsLen) ** dlcpiArma22hFit - arima(ausT2Ts[,4], order=c(2,1,2)) ** dlcpihArma22Fit * *Call: **arima(x = ausT2Ts[, 4], order = c(2, 1, 2), xreg = 1:dlcpihTsLen) * *Coefficients: ** ar1 ar2 ma1 ma2 1:dlcpihTsLen ** -0.1083 0.8673 0.5263 -0.3716 0.0146 **s.e. 0.0493 0.0484 0.0894 0.0852 0.0041 * *sigma^2 estimated as 0.0001282: log likelihood = 498.38, aic = -984.76* * * * * I wonder why the coefficient values are little bit different between them. * * Another thing I wonder is why the AIC value is so significantly different each other*.* * * Please help me, if anyone who have experience both of eview and R is in R community. 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] Plotting multiple vectors in one window?
Hi Caitlin, I would probably convert the data to a long format so bsa, unknown1, unknown2 are all in one variable and ditto for abs. Then control the plotting symbol using the variable indicator. abline() will just keep adding to the existing plot, so you could add all three lines of best fit using it with three separate calls. If you wanted to plot them staying in wide format, try using ?points ## example data (it is polite for the person asking for help to sample data (real or made up)) dat - as.data.frame(matrix(rnorm(60), ncol = 6)) colnames(dat) - c(bsa, unknown1, unknown2, abs, abs2, abs3) ## using a wide dataset. Note the use of with() to avoid retyping dat over and over ## each time I use reference one of the variables with(dat, { plot(bsa, abs, col='blue', pch=16, xlim=c(-3, 3), ylim=c(-3, 3), xlab = expression(paste(BSA, (, mu, g), sep=)), ylab=expression(A[595])) points(unknown1, abs2, col='blue', pch=17) points(unknown2, abs3, col='blue', pch=18) abline(lm(abs ~ bsa)) abline(lm(abs2 ~ unknown1)) abline(lm(abs3 ~ unknown2)) title(main=Quantifying Protein Content via Bradford Microassay, col='blue') }) ## A solution using long format with ggplot2 for graphing require(ggplot2) datlong - reshape(dat, varying = list(1:3, 4:6), v.names = c(bsa, abs), direction = long) datlong$time - factor(datlong$time) head(datlong) ## look at the first few rows ggplot(data = datlong, mapping = aes(x = bsa, y = abs, group = time)) + stat_smooth(aes(linetype = time), size = 1, method = lm, se=FALSE) + geom_point(aes(shape = time)) Cheers, Josh On Mon, Aug 29, 2011 at 9:53 PM, Caitlin bioprogram...@gmail.com wrote: Hi all. Using the following code: plot(bsa, abs, col='blue', pch=16, xlim=c(0, 25), ylim=c(0.0, 1.0), xlab = expression(paste(BSA, (, mu, g), sep=)), ylab=expression(A[595])) plot(unknown1, abs2, col='blue', pch=16, xlim=c(0, 25), ylim=c(0.0, 1.0), xlab = expression(paste(Unknown_1, (, mu, g), sep=)), ylab=expression(A[595])) plot(unknown2, abs3, col='blue', pch=16, xlim=c(0, 25), ylim=c(0.0, 1.0), xlab = expression(paste(Unknown_2, (, mu, g), sep=)), ylab=expression(A[595])) myline.fit - lm(abs ~ bsa) summary(myline.fit) abline(myline.fit) axis(side=1, col=gray, tck=1, lty=dotted) axis(side=2, col=gray, tck=1, lty=dotted) box() minor.tick(nx=2, ny=2, tick.ratio=0.5) title(main=Quantifying Protein Content via Bradford Microassay, col='blue') ...I have constructed three individual plots. Is there a convenient way to plot three vectors (not from a file) into one window? With three individual lines of best fit? Probably using three symbols, e.g., pch=16, 17, 18, to distinguish them. Thanks, ~Caitlin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Joshua Wiley Ph.D. Student, Health Psychology Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] R-Studio Question
Above the graph on the left there are back and forward arrows. You can use those (like a browser). This might have been better asked on the R-Studio forums. They're very friendly. best iain --- On Tue, 30/8/11, Eran Eidinger e...@taykey.com wrote: From: Eran Eidinger e...@taykey.com Subject: [R] R-Studio Question To: r-help@r-project.org Date: Tuesday, 30 August, 2011, 8:59 Hello, I've switched to R studio from the StatET Eclipse plug-in. I have a question regarding navigating between plots. When I use x11() or windows() new devices are created and I know how to switch back and forth between them. However, when I plot on the device that stands for R-Studio's built-in plot browser, is there a way to switch back between plots? Each new plot command opens a new plot, and the number of devices does not change. Thanks, Eran. [[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] Asking Favor For Remove element with Particular Value In Vector
On 08/30/2011 12:06 AM, Bert Gunter wrote: Jim et. al: This is the second time I've seen this advice recently. Use logical indexing: which(), though not wrong, is superfluous: x[ !x %in% c(0,255)] will do, rather than: By golly, you're right, and it works even if x is a logical vector. I should have checked the operator precedence. Jim __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] execute R commands from Matlab
They seem to have a workaround. I don't know whether anything better is available by now. http://www.mathworks.com/matlabcentral/newsreader/view_thread/163726 HTH, Daniel sarak wrote: Is it possible for anyone to upload a youtube video showing how to execute R commands in Matlab , it's so vital for me .. -- View this message in context: http://r.789695.n4.nabble.com/execute-R-commands-from-Matlab-tp3778263p3778281.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] execute R commands from Matlab
This seems to work, as well: http://www.mathworks.com/matlabcentral/fx_files/5051/1/content/Rdemo.html -- View this message in context: http://r.789695.n4.nabble.com/execute-R-commands-from-Matlab-tp3778263p3778282.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] ARMA show different result between eview and R
In your first line, you write ARMA(2,2). However, what you fit in R is ARIMA(2,1,2). What you fit in eview, I can't tell. Could that explain the difference? HTH, Daniel Young Gyu Park wrote: When I do ARMA(2,2) using one lag of LCPIH data This is eview result *Dependent Variable: DLCPIH **Method: Least Squares **Date: 08/12/11 Time: 12:44 **Sample (adjusted): 1970Q2 2010Q2 **Included observations: 161 after adjustments **Convergence achieved after 14 iterations **MA Backcast: 1969Q4 1970Q1 ** **VariableCoefficientStd. Errort-StatisticProb. ** **C0.0033610.0018141.8533520.0657 **DLCPIH(-1)-0.1001500.053160-1.8839170.0614 **DLCPIH(-2)0.8704560.05246616.590750. **MA(1)0.5322520.1001105.3166780. **MA(2)-0.3793830.099535-3.8115660.0002 ** **R-squared0.512067Mean dependent var0.014816 **Adjusted R-squared0.499556S.D. dependent var 0.016274 **S.E. of regression0.011513Akaike info criterion -6.060182 **Sum squared resid0.020676Schwarz criterion-5.964486 **Log likelihood492.8446Hannan-Quinn criter.-6.021326 **F-statistic40.92897Durbin-Watson stat2.012062 **Prob(F-statistic)0.00 ** **Inverted MA Roots .40 -.94 * This is R result * dlcpihTsLen - length(ausT2Ts[,4]) ** dlcpihArma22Fit - arima(ausT2Ts[,4], order=c(2,1,2), xreg=1:dlcpihTsLen) ** dlcpiArma22hFit - arima(ausT2Ts[,4], order=c(2,1,2)) ** dlcpihArma22Fit * *Call: **arima(x = ausT2Ts[, 4], order = c(2, 1, 2), xreg = 1:dlcpihTsLen) * *Coefficients: ** ar1 ar2 ma1 ma2 1:dlcpihTsLen ** -0.1083 0.8673 0.5263 -0.3716 0.0146 **s.e. 0.0493 0.0484 0.0894 0.0852 0.0041 * *sigma^2 estimated as 0.0001282: log likelihood = 498.38, aic = -984.76* * * * * I wonder why the coefficient values are little bit different between them. * * Another thing I wonder is why the AIC value is so significantly different each other*.* * * Please help me, if anyone who have experience both of eview and R is in R community. 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. -- View this message in context: http://r.789695.n4.nabble.com/ARMA-show-different-result-between-eview-and-R-tp3778217p3778299.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] R-Studio Question
I meant navigating through the command line, using R commands (like dev.set() for regular plots). Thank you for the reference, I will ask There. Eran. On Tue, Aug 30, 2011 at 11:37 AM, Iain Gallagher iaingallag...@btopenworld.com wrote: Above the graph on the left there are back and forward arrows. You can use those (like a browser). This might have been better asked on the R-Studio forums. They're very friendly. best iain --- On Tue, 30/8/11, Eran Eidinger e...@taykey.com wrote: From: Eran Eidinger e...@taykey.com Subject: [R] R-Studio Question To: r-help@r-project.org Date: Tuesday, 30 August, 2011, 8:59 Hello, I've switched to R studio from the StatET Eclipse plug-in. I have a question regarding navigating between plots. When I use x11() or windows() new devices are created and I know how to switch back and forth between them. However, when I plot on the device that stands for R-Studio's built-in plot browser, is there a way to switch back between plots? Each new plot command opens a new plot, and the number of devices does not change. Thanks, Eran. [[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] weird apply() behavior
#Do apply(y,1,print) #Note the space that is inserted before the 1. If you insert this space in your function apply(y,1,function(x){x-unlist(x); if (!is.na(x[2]) x[2]=='2k' !is.na(x[1]) x[1]==' 1') 1 else 0} ) #you get the result you expect. #Also, note that your !is.na conditions are redundant for the given example because if the other conditions are true, the !is.na conditions default to true, as well. apply(y,1,function(x){x-unlist(x); if (x[2]=='2k' x[1]==' 1') 1 else 0} ) HTH, Daniel -- View this message in context: http://r.789695.n4.nabble.com/weird-apply-behavior-tp3777699p3778318.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] Asking Favor For Remove element with Particular Value In Vector
But that is a good reason to always use parentheses: x[ !(x %in% c(0,255))] since some of the 'precendences' vary between languages. On Tue, Aug 30, 2011 at 4:47 AM, Jim Lemon j...@bitwrit.com.au wrote: On 08/30/2011 12:06 AM, Bert Gunter wrote: Jim et. al: This is the second time I've seen this advice recently. Use logical indexing: which(), though not wrong, is superfluous: x[ !x %in% c(0,255)] will do, rather than: By golly, you're right, and it works even if x is a logical vector. I should have checked the operator precedence. 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. -- 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] Plotting multiple vectors in one window?
-Original Message- From: r-help-boun...@r-project.org On Behalf Of Caitlin Subject: [R] Plotting multiple vectors in one window? ...I have constructed three individual plots. Is there a convenient way to plot three vectors (not from a file) into one window? ?points and then With three individual lines of best fit? abline() or predict(), depending on what kind of best fit you had in mind *** This email and any attachments are confidential. Any use...{{dropped:8}} __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Simulating distribution of max of two die
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Jaap van Wyk Sent: 30 August 2011 04:57 To: r-help@r-project.org Subject: [R] Simulating distribution of max of two die how to find the distribution of the maximum of rolling two balanced die. Is there perhaps a more elegant way to do this, other than the way I am using below? #Perhaps dice - matrix(sample(1:6, 4,replace=T), ncol=2) dice.max - apply(dice, 1, max) barplot(table(dice.max)) #and just for interest mids-barplot(table(dice.max)/length(dice.max)) #gives proportions all.pairs - expand.grid(1:6, 1:6) dice.max.exact - apply(all.pairs, 1, max) points(mids, table(dice.max.exact)/36, pch=_, cex=2, col=2) *** This email and any attachments are confidential. Any use...{{dropped:8}} __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Why does loading saved/cached objects add significantly to RAM consumption?
Dear list, I make use of cached objects extensively for time consuming computations and yesterday I happened to notice some very strange behavior in that respect: When I execute a given computation whose result I'd like to cache (tried both saving it as '.Rdata' and via package 'R.cache' which uses a own filetype '.Rcache'), my R session consumes about 200 MB of RAM, which is fine. Now, when I make use of the previously cached object (i.e. loading it, assigning it to a certain field of a Reference Class object), I noticed that RAM consumption of my R process jumps to about 250 MB! a Each new loading of cached/saved objects adds to that consumption (in total, I have about 5-8 objects that are processed this way), so at some point I easily get a RAM consumption of over 2 GB where I'm only at about 200 MB of consumption when I compute each object directly! Object sizes (checked with 'object.size()') remain fairly constant. What's even stranger: after loading cached objects and removing them (either via 'rm()' or by assigning a 'fresh' empty object to the respective Reference Class field, RAM consumption remains at this high level and never comes down again. I checked the behavior also in a small example which is a simplification of my use case and which you'll find below (checked both on Win XP and Win 7 32 bit). I couldn't quite reproduce an immediate increase in RAM consumption, but what I still find really strange is a) why do repeated 'load()' calls result in an increase in RAM consumption? b) why does the latter not go down again after the objects have been removed from '.GlobalEnv'? Did anyone of you experience a similar behavior? Or even better, does anyone know why this is happening and how it might be fixed (or be worked around)? ;-) I really need your help on this one as it's crucial for my thesis, thanks a lot for anyone replying!! Regards, Janko # EXAMPLE # setRefClass(A, fields=list(.PRIMARY=environment)) setRefClass(Test, fields=list(a=A)) obj.1 - lapply(1:5000, function(x){ rnorm(x) }) names(obj.1) - paste(sample, 1:5000, sep=.) obj.1 - as.environment(obj.1) test - new(Test, a=new(A, .PRIMARY=obj.1)) test$a$.PRIMARY$sample.10 #+ object.size(test) object.size(test$a) object.size(obj.1) # RAM used by R session: 118 MB save(obj.1, file=C:/obj.1.Rdata) # Results in an object of ca. 94 MB save(test, file=C:/test.Rdata) # Results in an object of ca. 94 MB # START A NEW R SESSION # load(C:/test.Rdata) # RAM consumption still fine at 115 - 118 MB # But watch how it goes up as we repeatedly load objects for(x in 1:5){ load(C:/test.Rdata) } for(x in 1:5){ load(C:/obj.1.Rdata) } # Somehow there seems to be an upper limit, though # Removing the objects does not bring down RAM consumption rm(obj.1) rm(test) ## Sys.info() sysname release Windows XP version nodename build 2600, Service Pack 3 ASHB-109C-02 machinelogin x86 wwa418 user wwa418 sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] codetools_0.2-8 tools_2.13.1 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ddply from plyr package - any alternatives?
Adam, because I did not have time to entirely test Do you (or does your company) have an automated test suite in place? R 2.10.0 is nearly two years old, and R 2.12.0 is nearly one. Matthew AdamMarczak adam.marc...@gmail.com wrote in message news:1314385041626-3771731.p...@n4.nabble.com... No, it's not much faster. I'd say it's faster about 10-15% in my case. I dont want neither plyr or data.table package because our software on the server does not support R version over 2.10 and both of them have dependency for R = 2.12. Also I do not want to use old archives because I did not have time to entirely test them as it was quick demand for workaround. Best regards, Adam. -- View this message in context: http://r.789695.n4.nabble.com/ddply-from-plyr-package-any-alternatives-tp3765936p3771731.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] Choropleth in R
You can use spplot from sp. Some examples: http://blog.revolutionanalytics.com/2009/10/geographic-maps-in-r.html http://ryouready.wordpress.com/2009/11/16/infomaps-using-r-visualizing-german-unemployment-rates-by-color-on-a-map/ http://news.mrdwab.com/2010/05/16/choropleth-party-with-r/ Best, Oscar. --- Oscar Perpiñán Lamigueiro Dpto. Ingeniería Eléctrica EUITI-UPM http://procomun.wordpress.com - Hi all, I would like to use R in order to generate a Heatmap/Choropleth overlaid on the UK map. Can someone please help with finding the right package/code? Any help is much appreciated. Best, Reza [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Help with the 'reshape' package
Hi all, I am reading previous posts and guidance on the 'reshape' package in order to solve the simple problem below. Thinking that this might be very trivial for most of you, I thought there could be a fast solution coming from you guys, and I´d be very thankful for that. I have a matrix with dates, companies, prices, just like DateCompany Price set-11 A 3 dez-11 A 3,2 jan-12 A 3,3 fev-12 A 2,7 mar-12 A 2,7 abr-12 A 2,8 mai-12 A 2,9 jun-12 A 3 jul-12 A 3,1 mar-12 B 5 abr-12 B 5,5 mai-12 B 5,7 jun-12 B 7 jul-12 B 6,6 dez-11 C 1 jan-12 C 1,1 fev-12 C 1,11 mar-12 C 1,2 abr-12 C 1,3 and I want to convert it into something like below (missing data can be zeros or NAs) A B C set-11 3 NA NA dez-11 3,2 NA 1 jan-12 3,3 NA 1,1 fev-12 2,7 NA 1,11 mar-12 2,7 5 1,2 abr-12 2,8 5,5 1,3 mai-12 2,9 5,7 NA jun-12 3 7 NA jul-12 3,1 6,6 NA Workspace is attached. Thanks in advance. This message and its attachments may contain confidential and/or privileged information. If you are not the addressee, please, advise the sender immediately by replying to the e-mail and delete this message. Este mensaje y sus anexos pueden contener información confidencial o privilegiada. Si ha recibido este e-mail por error por favor bórrelo y envíe un mensaje al remitente. Esta mensagem e seus anexos podem conter informação confidencial ou privilegiada. Caso não seja o destinatário, solicitamos a imediata notificação ao remetente e exclusão da mensagem.__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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 versions and PostScript files
On Fri, 22 Jul 2011, James Cloos wrote: Please do note the posting guide: the context you omitted (when explicitly asked not to) is in the thread starting: https://stat.ethz.ch/pipermail/r-help/2011-July/284352.html I suspect that a few s/def/bind def/ on that prologue might improve things a bit. No discernable difference on the viewers I tested. The ps R creates freely switches between the sRGB ABC space and setgray. That is a good thing; it helps ensure that black will be just black when sent to a CMYK device. Without that you can get CMY black from some devices. But it does complicate things. (CMYK devices often use CMY black rather than K black when the source is RGB black because it is better when printing contone images, such as photographs. But it just wastes ink and toner when printing charts and similar graphics.) I've not seen a printer driver which does that for many years. But remember that R's postscript() has origins in the mid-1990s. R's pdf() is newer (R 1.3.0, 2001) and even by then the optimization could safely be left to the driver. The best improvement would be to have R keep track of the last colorspace and only run the srgb procedure when switching from DeviceGray, rather than every time it changes the RGB colour. Actually no, as it can do that rather often. Consider the pairs plots of the iris data in demo(graphics): that does (1200 times) switch to red, blue or green fill circle switch to black draw circle outline. Some viewers are rather slow in running that procedure, and on those viewers this example is slow. Workarounds: 1) Use pdf(), where the viewers seem to cache colorspaces. 2) In R-patched, use colormodel=rgb-nogray, which never switches colorspace (srgb-nogray in R-devel). 3) In R-devel, use colormodel=rgb (rather than srgb) and give up the colour accuracy (if your viewer is not already set for sRGB) for speed. The SetColor() function in R/src/library/grDevices/src/devPS.c looks to be the place to do that. The Invalidate() function and the PostScriptDesc struct there also need to track any such changes. Hmm, you seem not to understand how the code works. The postscript macro /bg switches colour, and the macros /p3 and similar use different colorspaces during their execution. It isn't just SetColor as its setting may not be used immediately. -JimC -- James Cloos cl...@jhcloos.com OpenPGP: 1024D/ED7DAEA6 -- 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.
[R] url prep function (backslash issue)
Greeting R Community, I am a windows user so this problem may be specific to windows. I often want to source files from within R such as: C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10. To source this file I need to go through the path and replace all the backslashes (\) with forward slashes (/). I usually do this in MS Word using the replace option, however, I'd like to do this in R. Attempting to write a function to do this runs into problems: When I enter the following: readyPath - function(path){ z - gsub(\, /, path) return(z) } I get: readyPath - function(path){ + z - gsub(\, /, path) + return(z) + } + ...meaning R can't close the sequence (presumably because of the backslash which has special meaning). So I tried (\\): readyPath - function(path){ z - gsub(\\, /, path) return(z) }This allows the function to be stored as an object but I'm not sure if this is correct. When I try the function the backslash gets me again: readyPath(C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10) Error: '\U' used without hex digits in character string starting C:\U This is what I'd like the function to return: [1] C:/Users/Rinker/Desktop/Research Law/Data/School Data 09-10 I want a function in which I enter a path and it returns the path with backslashes replaced with forward slashes. Is there a way to make a function to do this? Windows 7 user R version 2.14 beta Thank you, Tyler Rinker [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with the 'reshape' package
Hi Hi all, I am reading previous posts and guidance on the 'reshape' package in order to solve the simple problem below. Thinking that this might be very trivial for most of you, I thought there could be a fast solution coming from you guys, and I´d be very thankful for that. I have a matrix with dates, companies, prices, just like Date Company Price set-11 A 3 dez-11 A 3,2 jan-12 A 3,3 fev-12 A 2,7 mar-12 A 2,7 abr-12 A 2,8 mai-12 A 2,9 jun-12 A 3 jul-12 A 3,1 mar-12 B 5 abr-12 B 5,5 mai-12 B 5,7 jun-12 B 7 jul-12 B 6,6 dez-11 C 1 jan-12 C 1,1 fev-12 C 1,11 mar-12 C 1,2 abr-12 C 1,3 and I want to convert it into something like below (missing data can be zeros or NAs) A B C set-11 3 NA NA dez-11 3,2 NA 1 jan-12 3,3 NA 1,1 fev-12 2,7 NA 1,11 mar-12 2,7 5 1,2 abr-12 2,8 5,5 1,3 mai-12 2,9 5,7 NA jun-12 3 7 NA jul-12 3,1 6,6 NA You have already melted data (long format). So simply cast cast(test, Date~Company) Using Price as value column. Use the value argument to cast to override this choice Date A BC 1 abr-12 2.8 5.5 1.30 2 dez-11 3.2 NA 1.00 3 fev-12 2.7 NA 1.11 4 jan-12 3.3 NA 1.10 5 jul-12 3.1 6.6 NA 6 jun-12 3.0 7.0 NA 7 mai-12 2.9 5.7 NA 8 mar-12 2.7 5.0 1.20 9 set-11 3.0 NA NA Shall be OK. Regards Petr Workspace is attached. Thanks in advance. This message and its attachments may contain confidential and/or privileged information. If you are not the addressee, please, advise the sender immediately by replying to the e-mail and delete this message. Este mensaje y sus anexos pueden contener información confidencial o privilegiada. Si ha recibido este e-mail por error por favor bórrelo y envíe un mensaje al remitente. Esta mensagem e seus anexos podem conter informação confidencial ou privilegiada. Caso não seja o destinatário, solicitamos a imediata notificação ao remetente e exclusão da mensagem.__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Error in f(x, ...) : could not find function f2
Hi all, I am getting the erro showed in the subject. I was strange the this becomes to happen after a computer restar. I think after the restart another function f2 was in memory and it scape from me. func - Vectorize(FUN= function(y, frac, rate, sad, samp=Poisson, trunc=0, ...){ f0 - function(y,frac,n) { f1 - function(y,frac,n){ dpois(y,frac*n) } dcom - paste(d,deparse(substitute(sad)),sep=) dots - c(as.name(n),list(...)) f2 - call(dcom,dots) f - function(n){ f1(y,frac,n)*f2(n) } myintegrate - function() { r - 0 r1 - 1 x1 - 0 dx - 20 while(r1 10e-500) { r1 - integrate(f,x1,x1+dx)$value r - r + r1 x1 - x1 + dx } integrate(f,x1,Inf)$valu } myintegrate() } f0(y,frac,n)/(1-f0(trunc,frac,n)) },y) func(10, 0.1, 0.1, exp) Any idea? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] url prep function (backslash issue)
You seem to be looking for chartr(\\, /, path) (and FAQ Q7.8) What does any of this have to do with 'url prep': URLs are never written with backslashes? On Tue, 30 Aug 2011, Tyler Rinker wrote: Greeting R Community, I am a windows user so this problem may be specific to windows. I often want to source files from within R such as: C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10. To source this file I need to go through the path and replace all the backslashes (\) with forward slashes (/). I usually do this in MS Word using the replace option, however, I'd like to do this in R. Attempting to write a function to do this runs into problems: When I enter the following: readyPath - function(path){ z - gsub(\, /, path) return(z) } I get: readyPath - function(path){ + z - gsub(\, /, path) + return(z) + } + ...meaning R can't close the sequence (presumably because of the backslash which has special meaning). So I tried (\\): readyPath - function(path){ z - gsub(\\, /, path) return(z) }This allows the function to be stored as an object but I'm not sure if this is correct. It isn't: please do read the help for gsub (\ is a metacharacter). When I try the function the backslash gets me again: readyPath(C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10) Error: '\U' used without hex digits in character string starting C:\U You cannot do that: you have to scan a file or escape \ This is what I'd like the function to return: [1] C:/Users/Rinker/Desktop/Research Law/Data/School Data 09-10 I want a function in which I enter a path and it returns the path with backslashes replaced with forward slashes. Is there a way to make a function to do this? ?normalizePath chartr(\\, /, path) Windows 7 user R version 2.14 beta Thank you, Tyler Rinker [[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. -- 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] Saving a graph
Chang Cheng, this question has been asked on this list for several times. I would suggest you search the list archive (http://r.789695.n4.nabble.com/R-help-f789696.html or www.rseek.com) prior to posting in the future. graph size many points pdf would give you at least 10 threads with detailed description. There are numerous solutions and most of them point into Dieters or Brian Ripleys directions. Jannis --- Dieter Menne dieter.me...@menne-biomed.de schrieb am Di, 30.8.2011: Von: Dieter Menne dieter.me...@menne-biomed.de Betreff: Re: [R] Saving a graph An: r-help@r-project.org Datum: Dienstag, 30. August, 2011 05:57 Uhr Gang Chen-4 wrote: However, my problem is that the file generated from a graph of fixed size is too large (in the order of 10MB) because of many data points in multiple scatterplots. Any suggestions? Generate pdf, open and save it in Adobe Acrobat which does a compression when the setting are correct. Dieter -- View this message in context: http://r.789695.n4.nabble.com/Saving-a-graph-tp3777456p3778015.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Conditional plots in the soiltexture package
Dear Julien It is exactly what I need. Thanks a lot. - Bc.Sc.Agri. Alessandro Samuel-Rosa Postgraduate Program in Soil Science Federal University of Santa Maria Av. Roraima, nº 1000, Bairro Camobi, CEP 97105-970 Santa Maria, Rio Grande do Sul, Brazil -- View this message in context: http://r.789695.n4.nabble.com/Conditional-plots-in-the-soiltexture-package-tp383p3778562.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] ATSP to TSP reformulation
Hi Ian, Your example runs for me without problems. It seems that you are using an older version of TSP. Please upgrade to the latest version TSP (update to TSP_1.0-3). I am using: sessionInfo() R version 2.13.1 (2011-07-08) Platform: i686-pc-linux-gnu (32-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TSP_1.0-3 loaded via a namespace (and not attached): [1] tools_2.13.1 Hint: use '-' instead of '=' for assignments. Regards, Michael -- Dr. Michael Hahsler, Visiting Assistant Professor Department of Computer Science and Engineering Lyle School of Engineering Southern Methodist University, Dallas, Texas (214) 768-8878 * mhahs...@lyle.smu.edu * http://lyle.smu.edu/~mhahsler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] url prep function (backslash issue)
Thank you Brian. When I wrote the email I typed url into the subject line by accident. I mean path. Thank you,Tyler Date: Tue, 30 Aug 2011 14:00:22 +0100 From: rip...@stats.ox.ac.uk To: tyler_rin...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] url prep function (backslash issue) You seem to be looking for chartr(\\, /, path) (and FAQ Q7.8) What does any of this have to do with 'url prep': URLs are never written with backslashes? On Tue, 30 Aug 2011, Tyler Rinker wrote: Greeting R Community, I am a windows user so this problem may be specific to windows. I often want to source files from within R such as: C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10. To source this file I need to go through the path and replace all the backslashes (\) with forward slashes (/). I usually do this in MS Word using the replace option, however, I'd like to do this in R. Attempting to write a function to do this runs into problems: When I enter the following: readyPath - function(path){ z - gsub(\, /, path) return(z) } I get: readyPath - function(path){ + z - gsub(\, /, path) + return(z) + } + ...meaning R can't close the sequence (presumably because of the backslash which has special meaning). So I tried (\\): readyPath - function(path){ z - gsub(\\, /, path) return(z) }This allows the function to be stored as an object but I'm not sure if this is correct. It isn't: please do read the help for gsub (\ is a metacharacter). When I try the function the backslash gets me again: readyPath(C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10) Error: '\U' used without hex digits in character string starting C:\U You cannot do that: you have to scan a file or escape \ This is what I'd like the function to return: [1] C:/Users/Rinker/Desktop/Research Law/Data/School Data 09-10 I want a function in which I enter a path and it returns the path with backslashes replaced with forward slashes. Is there a way to make a function to do this? ?normalizePath chartr(\\, /, path) Windows 7 user R version 2.14 beta Thank you, Tyler Rinker [[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. -- 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 [[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] Configuring Proxy: Proxy Authentication Required with --internet2
On 30/08/2011 3:48 AM, behave wrote: That was my first guess as well, but unfortunately this doesn't solve the problem. I is remarkably that IE requires authentification for every new instance I open (even if another instance is already open)... Any other hints? You can read about how WinINet can be made to handle authentication on this page: http://msdn.microsoft.com/en-us/library/aa384220%28v=vs.85%29.aspx (If that URL doesn't work, search for WinINet on microsoft.com, and navigate to Handling Authentication.) To do any of this would require changes to the file https://svn.r-project.org/R/trunk/src/modules/internet/internet.c. The USE_WININET_ASYNC macro is *not* defined, so ignore code in those ifdefs. You could try changing the error handling code around line 791. Since I don't use a proxy I can't test any of this and won't attempt it myself, but if you are able to make the changes and test them and they are reasonable looking, I'll consider incorporating them. Duncan Murdoch __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] url prep function (backslash issue)
Brian Ripley told you how to do the translation, but there's another problem: On 30/08/2011 8:14 AM, Tyler Rinker wrote: [ much deleted ] When I try the function the backslash gets me again: readyPath(C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10) The problem is that you haven't entered a string containing backslashes, you've tried to enter a string containing escapes. The parser sees a single backslash and attaches it to the next letter, so \U is taken to be the start of a Unicode character, and you get the error Error: '\U' used without hex digits in character string starting C:\U The way around this is to avoid the parser, by something like this: oldstring - readline() C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10 and then applying chartr to oldstring. Duncan Murdoch This is what I'd like the function to return: [1] C:/Users/Rinker/Desktop/Research Law/Data/School Data 09-10 I want a function in which I enter a path and it returns the path with backslashes replaced with forward slashes. Is there a way to make a function to do this? Windows 7 user R version 2.14 beta Thank you, Tyler Rinker [[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] Showing zero frequencies with xtabs
Thanks Peter Petr, It was indeed an issue of having some character variables in there. Now it works just fine. Cheers, Luca Il giorno 30/ago/2011, alle ore 10.15, peter dalgaard ha scritto: On Aug 30, 2011, at 10:04 , Luca Meyer wrote: Hi, Does anyone know how to show zero frequencies variable levels with the xtabs command? They show with the table(x,y) command but I need to apply weight to frequency tables and I also need to cbind several tables together, which implies that they all need to show the same number of rows. Are you sure you are doing the same thing as with table(). I'd expect it to work if you ensure that the variables are factors: library(ISwR) xtabs(~sex+menarche,data=juul) menarche sex 1 2 2 369 335 juul$sex - factor(juul$sex,levels=1:2) xtabs(~sex+menarche,data=juul) menarche sex 1 2 1 0 0 2 369 335 Alternatively, do you know how to column bind tables with different number of rows? I cannot use merge as it requires daata.frame and that modifies the look of the banner table I am trying to create... Thanks, Luca Mr. Luca Meyer www.lucameyer.com R version 2.13.1 (2011-07-08) Mac OS X 10.6.8 [[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. -- Peter Dalgaard, Professor Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] RES: Help with the 'reshape' package
Petr, many thanks. It´s very straightforward to to deal with the package, I had different sources of revenues for same company, same month, like below, and just by adding sum at the end of the function it collapsed values from all sources. Very useful! Cheers cast(dta, Data~Company, value=Revenues, sum) Date Company Revenues set-11A 3 dez-11A 3,2 jan-12A 3,3 fev-12A 2,7 mar-12A 2,7 abr-12A 2,8 mai-12A 2,9 jun-12A 3 jul-12A 3,1 mar-12B 5 abr-12B 5,5 mai-12B 5,7 jun-12B 7 jul-12B 6,6 dez-11C 1 jan-12C 1,1 fev-12C 1,11 mar-12C 1,2 abr-12C 1,3 dez-11A 0,2 jan-12A 4,3 fev-12A 2,1 mar-12A 2,2 A B C 01/09/2011 3 0 0 01/12/2011 3,4 0 1 01/01/2012 7,6 0 1,1 01/02/2012 4,8 0 1,11 01/03/2012 4,9 5 1,2 01/04/2012 2,8 5,5 1,3 01/05/2012 2,9 5,7 0 01/06/2012 3 7 0 01/07/2012 3,1 6,6 0 -Mensagem original- De: Petr PIKAL [mailto:petr.pi...@precheza.cz] Enviada em: terça-feira, 30 de agosto de 2011 09:28 Para: Filipe Leme Botelho Cc: r-help@r-project.org Assunto: Re: [R] Help with the 'reshape' package Hi Hi all, I am reading previous posts and guidance on the 'reshape' package in order to solve the simple problem below. Thinking that this might be very trivial for most of you, I thought there could be a fast solution coming from you guys, and I´d be very thankful for that. I have a matrix with dates, companies, prices, just like Date Company Price set-11 A 3 dez-11 A 3,2 jan-12 A 3,3 fev-12 A 2,7 mar-12 A 2,7 abr-12 A 2,8 mai-12 A 2,9 jun-12 A 3 jul-12 A 3,1 mar-12 B 5 abr-12 B 5,5 mai-12 B 5,7 jun-12 B 7 jul-12 B 6,6 dez-11 C 1 jan-12 C 1,1 fev-12 C 1,11 mar-12 C 1,2 abr-12 C 1,3 and I want to convert it into something like below (missing data can be zeros or NAs) A B C set-11 3 NA NA dez-11 3,2 NA 1 jan-12 3,3 NA 1,1 fev-12 2,7 NA 1,11 mar-12 2,7 5 1,2 abr-12 2,8 5,5 1,3 mai-12 2,9 5,7 NA jun-12 3 7 NA jul-12 3,1 6,6 NA You have already melted data (long format). So simply cast cast(test, Date~Company) Using Price as value column. Use the value argument to cast to override this choice Date A BC 1 abr-12 2.8 5.5 1.30 2 dez-11 3.2 NA 1.00 3 fev-12 2.7 NA 1.11 4 jan-12 3.3 NA 1.10 5 jul-12 3.1 6.6 NA 6 jun-12 3.0 7.0 NA 7 mai-12 2.9 5.7 NA 8 mar-12 2.7 5.0 1.20 9 set-11 3.0 NA NA Shall be OK. Regards Petr Workspace is attached. Thanks in advance. This message and its attachments may contain confidential and/or privileged information. If you are not the addressee, please, advise the sender immediately by replying to the e-mail and delete this message. Este mensaje y sus anexos pueden contener información confidencial o privilegiada. Si ha recibido este e-mail por error por favor bórrelo y envíe un mensaje al remitente. Esta mensagem e seus anexos podem conter informação confidencial ou privilegiada. Caso não seja o destinatário, solicitamos a imediata notificação ao remetente e exclusão da mensagem.__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. This message and its attachments may contain confidential and/or privileged information. If you are not the addressee, please, advise the sender immediately by replying to the e-mail and delete this message. Este mensaje y sus anexos pueden contener información confidencial o privilegiada. Si ha recibido este e-mail por error por favor bórrelo y envíe un mensaje al remitente. Esta mensagem e seus anexos podem conter informação confidencial ou privilegiada. Caso não seja o destinatário, solicitamos a imediata notificação ao remetente e exclusão da mensagem. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ATSP to TSP reformulation
Dr. Hahsler, Thank you so much for looking at my code. I made sure that I had TSP_1.0-3 install and ran the code again (this time with - instead of = for my assignments). I received the same response. I checked my sessionInfo and did not see anything out of the ordinary. Does anything look out of place to you? Thank you for your time. Here is my sessionInfo: R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] TSP_1.0-3 -- View this message in context: http://r.789695.n4.nabble.com/ATSP-to-TSP-reformulation-tp3777105p3778959.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] R cmd build error -- running 'zip' failed
Hi All, My attempts to build an R package on my Windows 7 computer using R V13.0 ir R V13.1 using R CMD build --binary filename have been failing at the penultimate step with the error message running 'zip' failed coming after the procedure has completed the MD5 sums step.The same build command on the same package completes successfully on my older Vista computer. Since I would prefer to do the builds on the Windows 7 computer I would appreciate any thoughts on why this maybe happening and what I can do to fix the problem. Thanks and best regards, Joel Pitt [[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] Exception while using NeweyWest function with doMC
On Aug 30, 2011, at 11:29 AM, Simon Zehnder wrote: Hi David, thank you very much for your advice! I updated R and all my packages. Regrettably it doesn't work yet. But, I think, that the parallel processing (using 32bit) does improve time, especially when it comes to higher dimensions: system.time(simuFunctionSeq(0.03, 0.015, 1, 5, 1000, 100,/Users/ simon/Documents/R/BigMTest)) system.time(simuFunctionPar(0.03, 0.015, 1, 5, 1000, 100,/Users/ simon/Documents/R/BigMTest)) [1] Sequential Processing with N = 1000 and K = 100 user system elapsed 5.157 0.086 5.587 [1] Parallel Processing with N = 1000 and K = 100 user system elapsed 6.069 0.220 3.895 : system.time(simuFunctionSeq(0.03, 0.015, 1, 5, 1, 100,/Users/ simon/Documents/R/BigMTest)) system.time(simuFunctionPar(0.03, 0.015, 1, 5, 1, 100,/Users/ simon/Documents/R/BigMTest)) [1] Sequential Processing with N = 1 and K = 100 user system elapsed 8.129 0.689 12.747 [1] Parallel Processing with N = 1 and K = 100 user system elapsed 8.387 0.772 12.005 : system.time(simuFunctionSeq(0.03, 0.015, 1, 5, 1, 1000,/ Users/simon/Documents/R/BigMTest)) system.time(simuFunctionPar(0.03, 0.015, 1, 5, 1, 1000,/Users/ simon/Documents/R/BigMTest)) [1] Sequential Processing with N = 1 and K = 1000 user system elapsed 71.295 6.330 109.656 [1] Parallel Processing with N = 1 and K = 1000 user system elapsed 50.943 6.347 89.115 Or are the times negligible? I would think that for most applications getting a gain of efficiency of 20% would be considered unworthy of the effort at setting up and maintaining. I suppose if a simulation ran for 18 hours in sequential mode and you would be happier if it were done in the morning after leaving overnight and finding it had completed in 15 hours, it might be worth the effort. What happens if I use a supercomputer with several cores and much more memory? Or even a MacPro with 4 or 8 cores and 32-64 GB?. Generally you hope to see halving or quartering in times when you apply these techniques. -- David. Thanks again! Simon On Aug 29, 2011, at 6:59 PM, David Winsemius wrote: On Aug 27, 2011, at 3:37 PM, Simon Zehnder wrote: Dear R users, I am using R right now for a simulation of a model that needs a lot of memory. Therefore I use the *bigmemory* package and - to make it faster - the *doMC* package. See my code posted on http://pastebin.com/dFRGdNrG Now, if I use the foreach loop with the addon %do% (for sequential run) I have no problems at all - only here and there some singularities in regressor matrices which should be ok. BUT if I run the loop on multiple cores I get very often a bad exception. I have posted the exception on http://pastebin.com/eMWF4cu0 The exception comes from the NeweyWest function loaded within the sandwich library. I have no clue, what it want to say me and why it is so weirdly printed to the terminal. I am used to receive here and there errorsbut the messages never look like this. Does anyone have a useful answer for me, where to look for the cause of this weird error? Here some additional information: Hardware: MacBook Pro 2.66 GHz Intel Core Duo, 4 GB Memory 1067 MHz DDR3 Software System: Mac Os X Lion 10.7.1 (11B26) Software App: R64 version 2.11.1 run via Mac terminal Using the R64 version in a 4GB environment will reduce the effective memory capacity since the larger pointers take up more space, and using parallel methods is unlikely to improve performance very much with only two cores. It also seems likely that there have been several bug fixes in the last couple of years since that version of R was released, so the package authors are unlikely to be very interested in segfault errors thrown by outdated software. I hope someone has a good suggestion! Update R. Don't use features that only reduce performance and make unstable a machine that has limited resources. -- 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] url prep function (backslash issue)
Duncan, Thanks. Combined with what Brian Ripley wrote it all works. For future thread searchers this worked: oldstring - readline() C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10 chartr(\\, /,oldstring) Thank you both,Tyler # Date: Tue, 30 Aug 2011 09:35:58 -0400 From: murdoch.dun...@gmail.com To: tyler_rin...@hotmail.com CC: r-help@r-project.org Subject: Re: [R] url prep function (backslash issue) Brian Ripley told you how to do the translation, but there's another problem: On 30/08/2011 8:14 AM, Tyler Rinker wrote: [ much deleted ] When I try the function the backslash gets me again: readyPath(C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10) The problem is that you haven't entered a string containing backslashes, you've tried to enter a string containing escapes. The parser sees a single backslash and attaches it to the next letter, so \U is taken to be the start of a Unicode character, and you get the error Error: '\U' used without hex digits in character string starting C:\U The way around this is to avoid the parser, by something like this: oldstring - readline() C:\Users\Rinker\Desktop\Research Law\Data\School Data 09-10 and then applying chartr to oldstring. Duncan Murdoch This is what I'd like the function to return: [1] C:/Users/Rinker/Desktop/Research Law/Data/School Data 09-10 I want a function in which I enter a path and it returns the path with backslashes replaced with forward slashes. Is there a way to make a function to do this? Windows 7 user R version 2.14 beta Thank you, Tyler Rinker [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] multi-response regression with random forest
Dear list, I performed a multivariate analysis on freshwater invertebrates data. So I obtained coordinates of my samples on the axes defining the first factorial plane (F1 and F2). I would like to see if the positions on my factorial plan could be linked to levels of impairment ('low' vs 'significant') for several water quality pressure categories and which pressure categories were the most important to explain my data. I first used random forests (package randomForest) to independently regressed the F1 and F2 coordinates against my pressures levels. These models explained around 13% of the variability for the first axis and 1.5% or the second axis. I heard about multi-response modelizations and tried to model the bi-variate response F1+F2 from the same set of pressure levels. This time, the model explained around 37% of the variability, that was great. But I don't understand what is precisely modeled in such multi-response regressions with random forest, when I used the predict() function on my data I obtained only one value for each sample. What correspond to this prediction? F1, F2, some combination of the both? Any advice and links to helpful litterature would be appreciated, Thanks, Cédric ___ Here is a small extract of my input data : ID F1 F2 WQ1 WQ2 WQ3 WQ4 423007 -0.181720936 -0.031683254 Impaired Impaired Impaired Impaired 423432 -0.013823243 -0.044562244 Good Good Impaired Good 382886 -0.062171083 0.095592402 Good Impaired Good Impaired 349067 0.165199490 -0.006247771 Impaired Good Impaired Good 350787 -0.086522253 -0.001156491 Good Good Impaired Good 423700 -0.094519496 0.058552236 Good Good Impaired Good 1473 -0.030547960 0.041201208 Good Good Impaired Good 422893 -0.381074618 -0.108488149 Good Good Good Good 424323 -0.200710868 0.008960769 Good Impaired Impaired Impaired 351117 -0.026336697 -0.011788642 Good Good Impaired Good 423356 -0.095307898 0.032821813 Good Good Impaired Good 52 0.181933163 -0.070008234 Good Good Good Good 529 0.201013553 -0.039925550 Good Good Good Good 123 0.049202307 -0.255373209 Good Good Good Good 424332 -0.201756587 -0.007161893 Good Good Impaired Good 423925 0.182053115 -0.163286598 Good Good Good Good 422967 0.009489423 0.078132841 Good Good Impaired Good 423899 0.042904501 0.022193773 Good Good Good Good 350912 0.031308796 0.066608196 Good Good Good Good 422988 -0.049664431 0.063449869 Good Good Impaired Good This is the formula I used for my model: mod=randomForest((F1+F2)~., data=data, ntree = 500, mtry = sqrt(ncol(data)-1)) The model summary: Call: randomForest(formula = (F1 + F2) ~ ., data = data, ntree = 500, mtry = sqrt(ncol(data) - 1)) Type of random forest: regression Number of trees: 500 No. of variables tried at each split: 4 Mean of squared residuals: 0.01772612 % Var explained: 37.98 And finally the predictions: prediction 423007 -0.256445319 423432 -0.078636802 382886 -0.088890538 349067 -0.118654211 350787 -0.112655013 423700 0.018815905 1473-0.032085983 422893 -0.303123232 424323 -0.226793376 351117 0.008599632 423356 -0.038947801 52 0.120712909 529 0.043381647 123 -0.087297539 424332 -0.180140229 423925 0.078654535 422967 -0.012138644 423899 0.078367004 350912 0.078654535 422988 0.014915818 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] character vector to text with returns
Hello, I need to clarify, Henrique's suggestion worked great for getting the text that I needed via cat(), but I haven't sorted out how to get cat() like output into a variable so I can pass it into the message body variable I am using. Here is what I mean: x [1] a b c d paste(x,collapse='\n') [1] a\nb\nc\nd y = paste(x,collapse='\n') cat(y) a b c d This is the problem with 'y' has the msg body: paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a\nb\nc\nd') This is what I am after (I think!): paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a b c d') Here is how I am actually using it (with sensitive items generalized): require(rJython) rJython - rJython() rJython$exec( import smtplib ) rJython$exec(from email.MIMEText import MIMEText) rJython$exec(import email.utils) mail-c( #Email settings fromaddr = 'ccqu...@gmail.com', toaddrs = 'userna...@somethinghere.com', #msg = MIMEText('test message from R'), paste(msg = MIMEText(',y,'),sep=),# my message in this example is 'y' msg['From'] = email.utils.formataddr(('gmail acct', fromaddr)), msg['To'] = email.utils.formataddr(('cc email!', toaddrs)), msg['Subject'] = 'test with y', #SMTP server credentials username = 'ccqu...@gmail.com', password = 'a password here', #Set SMTP server and send email, e.g., google mail SMTP server server = smtplib.SMTP('smtp.gmail.com:587'), server.ehlo(), server.starttls(), server.ehlo(), server.login(username,password), server.sendmail(fromaddr, toaddrs, msg.as_string()), server.quit()) jython.exec(rJython,mail) # and here is the error I get. Error in ls(envir = envir, all.names = private) : invalid 'envir' argument Just in case someone asks, I can do this: y = a test ...and the above email sends fine with 'a test' as the msg body. Any ideas? PS - I received lots of suggestions. Thank you very much for your effort/input. Ben On Mon, Aug 29, 2011 at 9:29 PM, Bert Gunter gunter.ber...@gene.com wrote: Is something like this what you want? x - letters[1:4] x y -do.call(paste,c( paste('',x[1]), as.list(x[2:3]), paste(x[4],''),sep=\n)) y cat(y,\n) -- Bert On Mon, Aug 29, 2011 at 6:59 PM, Ben qant ccqu...@gmail.com wrote: Unfortunately that didn't work. I just says the text is an invalid argument. I also tried saving it in a variable name and passed that in, but that didn't work. I get: Error in ls(envir = envir, all.names = private) : invalid 'envir' argument ...when I try to send the message. Any other ideas? Thanks, Ben On Mon, Aug 29, 2011 at 6:01 PM, Henrique Dallazuanna www...@gmail.com wrote: Try: paste(c(a, b, c), collapse = \n) On Mon, Aug 29, 2011 at 8:56 PM, Ben qant ccqu...@gmail.com wrote: Hello, Does anyone know how to convert this: msg [1] a [2] b [3] c To: msg a b c In other words, I need to convert a character vector to a single string with carriage returns for each row. Functionally, I'm attempting to send an email of a character vector in a way that is readable in the email body. I can only input one string as the message body parameter. I'm using rJython to send the email because I need authentication. Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Men by nature long to get on to the ultimate truths, and will often be impatient with elementary studies or fight shy of them. If it were possible to reach the ultimate truths without the elementary studies usually prefixed to them, these would not be preparatory studies but superfluous diversions. -- Maimonides (1135-1204) Bert Gunter Genentech Nonclinical Biostatistics [[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] Negative length vector error in simple merge
Hi, I'm trying to take a vector (length almost 2,000,000) and merge it with a data frame of the same length. I'm trying to do it solely based on index, and not any other factors. The vector is called offense, and the data frame is just called data. I went with the simplest option: merge(data,offense) but it always gives me the same error: Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) : negative length vectors are not allowed Solutions that haven't worked: - Changing offense into a data frame - Data doesn't exceed the 2^31 (2 billion) limit for length. When combined with offense, it will have about 68 million items total Thanks! DL -- View this message in context: http://r.789695.n4.nabble.com/Negative-length-vector-error-in-simple-merge-tp3778980p3778980.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] test message
Please ignore this message. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Help with the 'reshape' package
On Tue, Aug 30, 2011 at 7:42 AM, Filipe Leme Botelho filipe.bote...@vpar.com.br wrote: Hi all, I am reading previous posts and guidance on the 'reshape' package in order to solve the simple problem below. Thinking that this might be very trivial for most of you, I thought there could be a fast solution coming from you guys, and I´d be very thankful for that. Here is a zoo solution: # first set up input Lines - DateCompany Price set-11 A 3 dez-11 A 3,2 jan-12 A 3,3 fev-12 A 2,7 mar-12 A 2,7 abr-12 A 2,8 mai-12 A 2,9 jun-12 A 3 jul-12 A 3,1 mar-12 B 5 abr-12 B 5,5 mai-12 B 5,7 jun-12 B 7 jul-12 B 6,6 dez-11 C 1 jan-12 C 1,1 fev-12 C 1,11 mar-12 C 1,2 abr-12 C 1,3 Sys.setlocale(LC_ALL, Portuguese) library(zoo) # The read.zoo command converts first column to yearmon class # and reads it into a zoo object. # in next line we would normally # replace textConnection(Lines) with file name, e.g. myfile.txt # but here we do it this way to keep it self contained z - read.zoo(textConnection(Lines), header = TRUE, dec = ,, split = 2, FUN = function(x) as.yearmon(x, format = %b-%y)) This gives the following zoo object: z A BC set 2011 3.0 NA NA dez 2011 3.2 NA 1.00 jan 2012 3.3 NA 1.10 fev 2012 2.7 NA 1.11 mar 2012 2.7 5.0 1.20 abr 2012 2.8 5.5 1.30 mai 2012 2.9 5.7 NA jun 2012 3.0 7.0 NA It may be more convenient to keep as a zoo object so you can do other time series manipulations, e.g. plot(z) plot(z, screen = 1) but you want it as a data frame: DF - data.frame(Date = time(z), coredata(z)) -- 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.
[R] GMM with panel data
Hi everyone, I´m starting with GMM estimator for panel data in R. In fact Im starting with GMM estimation with panel data, my research area is accounting and finance, so Ive been reading many «econometric» books but I have some difficulties in applying GMM estimation. Ive also read the article «Panel data econometrics in R: the plm package» (Croissant Millo) and my question is: Does the pggm() function performs the estimation based in Arellano and Bond (1991)? If yes, is there any way to perform the estimation based in Blundell and Bond (1998) (that seems to be a better estimator)? Thank you, Cecília Carmo (Universidade de Aveiro) [[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] Exception while using NeweyWest function with doMC
Hi Jay, first: thank u very much for your comments! U made some very important points clear. I tried immediately to write directly the sample function from trade-as.big.matrix(matrix(sample(c(1,-1), (N+1)*K, replace=TRUE),ncol=K), backingpath=backingpath, backingfile=trade.bin,descriptorfile=trade.desc) into the big matrix: trade-big.matrix(sample(c(1,-1), (10+1), replace=TRUE),nrow=(10+1), ncol=10, type=double,backingpath=/Users/simon/Documents/R/BigMTest/, backingfile=terminaltest.bin, descriptorfile=terminaltest.desc) But I either get only 1s: trade[,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,]111111111 1 [2,]111111111 1 [3,]111111111 1 [4,]111111111 1 [5,]111111111 1 [6,]111111111 1 [7,]111111111 1 [8,]111111111 1 [9,]111111111 1 [10,]111111111 1 [11,]111111111 1 or only -1s: trade[,] [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [1,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [2,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [3,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [4,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [5,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [6,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [7,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [8,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [9,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [10,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 [11,] -1 -1 -1 -1 -1 -1 -1 -1 -1-1 Is there another possibility? In addition I found under ?as.big.matrix, for the second example the usage of matrix() inside of as.big.matrix(). But if I understood u correctly: usage is possible but does not save memory? I used the big.memory package because I always got - using simply matrix() - exceptions, telling me, that memory has reached its limits. After using big.memory all worked fine, BUT running http://pastebin.com/UxSkzrae and http://pastebin.com/MErGQsQd , I got this: http://pastebin.com/KrEncrSz. It seems, as there is a problem with memory allocation inside the underlying C-code, maybe a result from my matrix generation inside of the big matrix? Any suggestions? On Aug 29, 2011, at 6:24 PM, Jay Emerson wrote: Simon, Though we're please to see another use of bigmemory, it really isn't clear that it is gaining you anything in your example; anything like as.big.matrix(matrix(...)) still consumes full RAM for both the inner matrix() and the new big.matrix -- is the filebacking really necessary. It also doesn't appear that you are making use of shared memory, so I'm unsure what the gains are. However, I don't have any particular insight as to the subsequent problem with NeweyWest (which doesn't seem to be using the big.matrix objects). Jay -- Message: 32 Date: Sat, 27 Aug 2011 21:37:55 +0200 From: Simon Zehnder simon.zehn...@googlemail.com To: r-help@r-project.org Subject: [R] Exception while using NeweyWest function with doMC Message-ID: cagqvrp_gk+t0owbv1ste-y0zafmi9s_zwqrxyxugsui18ms...@mail.gmail.com Content-Type: text/plain Dear R users, I am using R right now for a simulation of a model that needs a lot of memory. Therefore I use the *bigmemory* package and - to make it faster - the *doMC* package. See my code posted on http://pastebin.com/dFRGdNrG snip - -- John W. Emerson (Jay) Associate Professor of Statistics Department of Statistics Yale University http://www.stat.yale.edu/~jay [[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] R crash
Dear users, By running the script below, R crashes systematically at the last command, namely dev.off(), on Windows 7, but not on Windows XP. I therefore don't provide a reproducible example and do not really extract the relevant parts of the script because it has most likely nothing to do with the script itself. I can do it though if you think it might be relevant. R crashes on Windows 7, sessionInfo(): R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] doBy_4.4.0 MASS_7.3-13snow_0.3-7 lme4_0.999375-41 [5] Matrix_0.9996875-3 lattice_0.19-30multcomp_1.2-7 mvtnorm_0.9-9991 [9] R2HTML_2.2 survival_2.36-9RSvgDevice_0.6.4.1 R.utils_1.7.8 [13] R.oo_1.8.1 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.13.1 nlme_3.1-101 stats4_2.13.1 But it works perfectly on Windows XP, sessionInfo(): R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] doBy_4.4.0 MASS_7.3-14snow_0.3-6 lme4_0.999375-41 [5] Matrix_0.9996875-3 lattice_0.19-33multcomp_1.2-7 mvtnorm_0.9-9991 [9] R2HTML_2.2 survival_2.36-9RSvgDevice_0.6.4.1 R.utils_1.7.8 [13] R.oo_1.8.1 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] grid_2.13.1 nlme_3.1-102 stats4_2.13.1 Except the locale, I don't see any difference and I don't really understand how that would make R crash by running dev.off(). Is there anything else than sessionInfo()? Thank you for your help, Ivan script - library(R.utils) library(RSvgDevice) library(doBy) primate_med - loadObject(primate_med.Rbin) select - primate_med #data object to use seq.yvar - c(5,12,8,9) ind.xvar - 4 filename - paste(regression, names(datobj)[ind.xvar], paste(names(datobj)[seq.yvar],collapse=_), paste(selvarstr,collapse=_), sep=_) filename - gsub(.median, , filename) select_mean - summaryBy(as.formula(paste(.~,names(select)[ind.xvar])), data=select, FUN=mean) devSVG(file=paste(filename, .svg, sep=)) par(mfrow=c(2,2)) diff_len - length(select)-length(select_mean) for (i in seq_along(seq.yvar)){ k - seq.yvar[i] plot(select[[k]]~select[[ind.xvar]], type=p, pch=1, xlab=names(select)[ind.xvar], ylab=names(select)[k], las=1) points(select_mean[[ind.xvar-diff_len]], select_mean[[k-diff_len]], pch=18, cex=2) two_reg(dat=select, xvar=ind.xvar, yvar=k) } dev.off() - -- Ivan CALANDRA PhD Student University of Hamburg Biozentrum Grindel und Zoologisches Museum Dept. Mammalogy Martin-Luther-King-Platz 3 D-20146 Hamburg, GERMANY +49(0)40 42838 6231 ivan.calan...@uni-hamburg.de ** http://www.for771.uni-bonn.de http://webapp5.rrz.uni-hamburg.de/mammals/eng/1525_8_1.php __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Negative length vector error in simple merge
On Aug 30, 2011, at 11:08 AM, DimmestLemming wrote: Hi, I'm trying to take a vector (length almost 2,000,000) and merge it with a data frame of the same length. I'm trying to do it solely based on index, and not any other factors. The vector is called offense, and the data frame is just called data. Bad name. There is a function named 'data'. I went with the simplest option: merge(data,offense) It wouldn't make much sense to merge a vector with a dataframe. The matching column should not appear any different except perhaps shorter. Sounds like you want cbind() rather than merge. (You really should have posted str(.) on both objects.) -- David. but it always gives me the same error: Error in rep.int(rep.int(seq_len(nx), rep.int(rep.fac, nx)), orep) : negative length vectors are not allowed Solutions that haven't worked: - Changing offense into a data frame - Data doesn't exceed the 2^31 (2 billion) limit for length. When combined with offense, it will have about 68 million items total Thanks! DL -- View this message in context: http://r.789695.n4.nabble.com/Negative-length-vector-error-in-simple-merge-tp3778980p3778980.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] algorithm to merge same entries in a matrix
Hi, I have the following, rather unorthodox problem: I have a matrix that looks like this: m1 - matrix(c('a','b','d',NA,'c','c'), 2,3, byrow=TRUE) [,1] [,2] [,3] [1,] a b d [2,] NA c c now I would like to transform this matrix into this matrix: [,1] [,2] [,3] [,4] [1,] a b c d [2,] NA NA NA NA so the rule is: if I find the same value (above: 'c') in neighbored cells (here: row wise) put this value in row 1 in a new column between column of neighbor a and column of neighbor b. too make it even more complicated: the definition of neighbored cells is not exclusively row wise. So for example I could encounter this kind of matrix: m2 - matrix(c('a','b','d',NA,NA,'c',NA, 'c', NA), 3,3, byrow=TRUE) [,1] [,2] [,3] [1,] a b d [2,] NA NA c [3,] NA c NA which should also be transformed into: [,1] [,2] [,3] [,4] [1,] a b c d [2,] NA NA NA NA (or m3 - matrix(c('a','b','d',NA,'c',NA,NA, NA, 'c'), 3,3, byrow=TRUE) ). Can perhaps someone give me some hints how to solve this efficiently? I think I could solve that with some loops … but I also need to make sure that it is efficient / not taking too much time. 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] R cmd build error -- running 'zip' failed
On 30/08/2011 11:05 AM, Pitt, Joel wrote: Hi All, My attempts to build an R package on my Windows 7 computer using R V13.0 ir R V13.1 using R CMD build --binaryfilename have been failing at the penultimate step with the error message running 'zip' failed coming after the procedure has completed the MD5 sums step.The same build command on the same package completes successfully on my older Vista computer. Since I would prefer to do the builds on the Windows 7 computer I would appreciate any thoughts on why this maybe happening and what I can do to fix the problem. Sounds like a problem with your PATH. Duncan Murdoch Thanks and best regards, Joel Pitt [[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] character vector to text with returns
Hello, (Sorry if this is a dup post...) I need to clarify, Henrique's suggestion worked great for getting the text that I needed via cat(), but I haven't sorted out how to get cat() like output into a variable so I can pass it into the message body variable I am using. Here is what I mean: x [1] a b c d paste(x,collapse='\n') [1] a\nb\nc\nd y = paste(x,collapse='\n') cat(y) a b c d This is the problem with 'y' has the msg body: paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a\nb\nc\nd') This is what I am after (I think!): paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a b c d') Here is how I am actually using it (with sensitive items generalized): require(rJython) rJython - rJython() rJython$exec( import smtplib ) rJython$exec(from email.MIMEText import MIMEText) rJython$exec(import email.utils) mail-c( #Email settings fromaddr = 'ccqu...@gmail.com', toaddrs = 'userna...@somethinghere.com' - Show quoted text - jython.exec(rJython,mail) # and here is the error I get. Error in ls(envir = envir, all.names = private) : invalid 'envir' argument Just in case someone asks, I can do this: y = a test ...and the above email sends fine with 'a test' as the msg body. Any ideas? PS - I received lots of suggestions. Thank you very much for your effort/input. Ben On Mon, Aug 29, 2011 at 6:01 PM, Henrique Dallazuanna www...@gmail.comwrote: Try: paste(c(a, b, c), collapse = \n) On Mon, Aug 29, 2011 at 8:56 PM, Ben qant ccqu...@gmail.com wrote: Hello, Does anyone know how to convert this: msg [1] a [2] b [3] c To: msg a b c In other words, I need to convert a character vector to a single string with carriage returns for each row. Functionally, I'm attempting to send an email of a character vector in a way that is readable in the email body. I can only input one string as the message body parameter. I'm using rJython to send the email because I need authentication. Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Negative length vector error in simple merge
Thanks! I'd just never heard of cbind or rbind... bit new. -- View this message in context: http://r.789695.n4.nabble.com/Negative-length-vector-error-in-simple-merge-tp3778980p3779267.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] character vector to text with returns
On Aug 30, 2011, at 1:09 PM, Ben qant wrote: Hello, (Sorry if this is a dup post...) I need to clarify, Henrique's suggestion worked great for getting the text that I needed via cat(), but I haven't sorted out how to get cat() like output into a variable so I can pass it into the message body variable I am using. cat() is not the right function to get text assgned to an object. It's entire purpose is to have a side-effect and _not_ return anything into R's workspace. Why are you not assigning the result of that paste operation to the variable? Here is what I mean: x [1] a b c d paste(x,collapse='\n') [1] a\nb\nc\nd y = paste(x,collapse='\n') cat(y) a b c d This is the problem with 'y' has the msg body: paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a\nb\nc\nd') This is what I am after (I think!): paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a b c d') Here is how I am actually using it (with sensitive items generalized): require(rJython) rJython - rJython() rJython$exec( import smtplib ) rJython$exec(from email.MIMEText import MIMEText) rJython$exec(import email.utils) mail-c( #Email settings fromaddr = 'ccqu...@gmail.com', toaddrs = 'userna...@somethinghere.com' - Show quoted text - jython.exec(rJython,mail) # and here is the error I get. Error in ls(envir = envir, all.names = private) : invalid 'envir' argument Just in case someone asks, I can do this: y = a test ...and the above email sends fine with 'a test' as the msg body. Any ideas? PS - I received lots of suggestions. Thank you very much for your effort/input. Ben On Mon, Aug 29, 2011 at 6:01 PM, Henrique Dallazuanna www...@gmail.com wrote: Try: paste(c(a, b, c), collapse = \n) On Mon, Aug 29, 2011 at 8:56 PM, Ben qant ccqu...@gmail.com wrote: Hello, Does anyone know how to convert this: msg [1] a [2] b [3] c To: msg a b c In other words, I need to convert a character vector to a single string with carriage returns for each row. Functionally, I'm attempting to send an email of a character vector in a way that is readable in the email body. I can only input one string as the message body parameter. I'm using rJython to send the email because I need authentication. Thanks! [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. 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] having trouble extracting week from chron object
Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts dts.chron - as.chron(dts) dts.chron class(dts.chron) # all of these component extractions work: months(dts.chron) weekdays(dts.chron) years(dts.chron) quarters(dts.chron) # but weeks() doesn't seem to work weeks(dts.chron) ?chron tells me: . . . The functions days(), months(), quarters(), years(), weeks(), weekdays(), hours(), minutes(), and seconds() take any chron object as input and extract the corresponding time interval . . . . Any advice? Thanks. Chris Ryan SUNY Upstate Medical University Clinical Campus at Binghamton Binghamton, NY __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Negative length vector error in simple merge
-Original Message- From: r-help-boun...@r-project.org [mailto:r-help-bounces@r- project.org] On Behalf Of DimmestLemming Sent: Tuesday, August 30, 2011 10:20 AM To: r-help@r-project.org Subject: Re: [R] Negative length vector error in simple merge Thanks! I'd just never heard of cbind or rbind... bit new. If you had never heard of cbind or rbind, then would be doing yourself a BIG favor by reading the Introduction to R that comes with every copy of R. Dan Daniel J. Nordlund Washington State Department of Social and Health Services Planning, Performance, and Accountability Research and Data Analysis Division Olympia, WA 98504-5204 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] column names with rbind loop
Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this: all.files - list.files() all.files [1] 1.rpkm 10.rpkm 11.rpkm 12.rpkm 13.rpkm 14.rpkm [7] 15.rpkm 16.rpkm 17.rpkm 18.rpkm 19.rpkm 2.rpkm [13] 3.rpkm 4.rpkm 5.rpkm 6.rpkm 7.rpkm 8.rpkm [19] 9.rpkm Then loop through them like this: new.data - NULL for(i in all.files) { + in.data - read.table(i) + new.data - rbind(new.data, in.data)} head(new.data) V1 V2V3 V4 V5V6 V7 1 seq_id source type startend score strand 2 scaffold_1 Ptrichocarpav2_0 gene_body 12639 13384 . + 3 scaffold_1 Ptrichocarpav2_0 gene_body 22190 22516 . + 4 scaffold_1 Ptrichocarpav2_0 gene_body 74076 75893 . + 5 scaffold_1 Ptrichocarpav2_0 gene_body 80207 81289 . - 6 scaffold_1 Ptrichocarpav2_0 gene_body 105236 107712 . + As you can see, R is putting a V1, V2... header row here because I didn't say header=TRUE in my read.table command. But if I do this within the loop, I get an error. If I try to delete the V1, V2 row after the fact by new.data - new.data[-1,] R deletes my real header row. How can I get the header that I want? Thanks for any help, --Kelly V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Gradient function in OPTIMX
Hi Kathie, The gradient check in optimx checks if the user specified gradient (at starting parameters) is within roughly 1.e-05 * (1 + fval) of the numerically computed gradient. It is likely that you have correctly coded up the gradient, but still there can be significant differences b/w numerical and exact gradients. This can happen when the gradients are very large. I would check this again separately as follows: require(numDeriv) mygrad - gr.fy(theta0) numgrad - grad(x=theta0, func=gr.fy) cbind(mygrad, numgrad) all.equal(mygrad, numgrad) Can you report these gradients to us? In optimx, we should probably change this into a warning rather than a stop. Ravi. --- Ravi Varadhan, Ph.D. Assistant Professor, Division of Geriatric Medicine and Gerontology School of Medicine Johns Hopkins University Ph. (410) 502-2619 email: rvarad...@jhmi.edu __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] having trouble extracting week from chron object
Well, there is no function called weeks in chron. Funny that the help mentions it. You can, however, use normal POSIXct objects and extract the week with: dts - dates(c(02/27/92, 02/27/92)) dts.posx - as.POSIXct(dts) result - as.integer(format(dts.posx,format=%W)) HTH Jannis --- Christopher W Ryan cr...@binghamton.edu schrieb am Di, 30.8.2011: Von: Christopher W Ryan cr...@binghamton.edu Betreff: [R] having trouble extracting week from chron object An: R-help@r-project.org Datum: Dienstag, 30. August, 2011 17:36 Uhr Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts dts.chron - as.chron(dts) dts.chron class(dts.chron) # all of these component extractions work: months(dts.chron) weekdays(dts.chron) years(dts.chron) quarters(dts.chron) # but weeks() doesn't seem to work weeks(dts.chron) ?chron tells me: . . . The functions days(), months(), quarters(), years(), weeks(), weekdays(), hours(), minutes(), and seconds() take any chron object as input and extract the corresponding time interval . . . . Any advice? Thanks. Chris Ryan SUNY Upstate Medical University Clinical Campus at Binghamton Binghamton, NY __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] having trouble extracting week from chron object
On Aug 30, 2011, at 1:36 PM, Christopher W Ryan wrote: Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts dts.chron - as.chron(dts) dts.chron class(dts.chron) # all of these component extractions work: months(dts.chron) weekdays(dts.chron) years(dts.chron) quarters(dts.chron) # but weeks() doesn't seem to work It doesn't work for me either but since I also have the package lubridate loaded, and ?weeks brings up a lubridate help page, I don't feel I have any right to complain. I get an error message what did you get?: Error in Ops.dates(pieces$week, 7) : * not defined for chron objects If I were posting I would also have had the good sense to include the output of sessionInfo(). weeks(dts.chron) Try type just: weeks # I get a lubridate function. ?chron tells me: Bur what does ?weeks tell you? . . . The functions days(), months(), quarters(), years(), weeks(), weekdays(), hours(), minutes(), and seconds() take any chron object as input and extract the corresponding time interval . . . . Any advice? Thanks. Chris Ryan SUNY Upstate Medical University Clinical Campus at Binghamton Binghamton, NY __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] RPostgreSQL Loading Issues
I'm starting to seriously use R and have tried to solve this issue using my reference books but I'm missing something simple. Running R-2.13.1 on Slackware-13.1. Trying to invoke RPostgreSQL so I can copy data from a postgres table to an R data-frame. I installed RPostgreSQL and the library() command shows it's present: Packages in library '/home/rshepard/R/i486-slackware-linux-gnu-library/2.13': DBI R Database Interface RPostgreSQL R interface to the PostgreSQL database system Yet, trying to load it fails: library(RPostgreSQL) Loading required package: DBI Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/rshepard/R/i486-slackware-linux-gnu-library/2.13/RPostgreSQL/libs/RPostgreSQL.so': libR.so: cannot open shared object file: No such file or directory Error: package/namespace load failed for 'RPostgreSQL' The shared library, of course, is present: [rshepard@salmo ~/R/i486-slackware-linux-gnu-library/2.13/RPostgreSQL/libs]$ ll -rwxr-xr-x 1 rshepard users 44385 2011-08-03 20:13 RPostgreSQL.so* Can someone explain to me what's going on and how I fix it? Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] lubridate and intervals
Hiya, maybe there is a native R function for this and if so please let me know! I have 2 data.frames with start and end dates, they read in as strings and I am converting to POSIXct. How can I check for overlap? The end result ideally will be a single data.frame containing all the columns of the other two with rows where there were date overlaps. df1-data.frame(start=as.POSIXct(paste('2011-06-01 ',1:20,':00',sep='')), end=as.POSIXct(paste('2011-06-01 ',1:20,':30',sep=''))) df2-data.frame(start=as.POSIXct(paste('2011-06-01 ',rep(seq(1,20,2),2),':',sample(1:19,20,replace=T),sep='')), end=as.POSIXct(paste('2011-06-01 ',rep(seq(1,20,2),2),':',sample(20:50,20),sep=''))) I tried: library(lubridate) df1$interval-new_interval(df1$start,df1$end) df1$interval[1] [1] 2011-06-01 01:00:00 -- 2011-06-01 01:30:00 df2$start[1] [1] 2011-06-01 01:17:00 PDT but df2$start[1] %in% df1$interval[1] [1] FALSE This must be fairly straight forward and I just don't know where to look! Thanks, Justin [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] character vector to text with returns
David, Yes, I understand that cat() won't do what I want, but that is the only way I can illustrate what I am after. Note the phrasing in my question: '...cat() like...' Regarding assigning the paste to a variable: it produces the same error. I've already tried that. Thanks for your suggestion! Ben On Tue, Aug 30, 2011 at 11:24 AM, David Winsemius dwinsem...@comcast.netwrote: On Aug 30, 2011, at 1:09 PM, Ben qant wrote: Hello, (Sorry if this is a dup post...) I need to clarify, Henrique's suggestion worked great for getting the text that I needed via cat(), but I haven't sorted out how to get cat() like output into a variable so I can pass it into the message body variable I am using. cat() is not the right function to get text assgned to an object. It's entire purpose is to have a side-effect and _not_ return anything into R's workspace. Why are you not assigning the result of that paste operation to the variable? Here is what I mean: x [1] a b c d paste(x,collapse='\n') [1] a\nb\nc\nd y = paste(x,collapse='\n') cat(y) a b c d This is the problem with 'y' has the msg body: paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a\nb\nc\nd') This is what I am after (I think!): paste(msg = MIMEText(',y,'),sep=) [1] msg = MIMEText('a b c d') Here is how I am actually using it (with sensitive items generalized): require(rJython) rJython - rJython() rJython$exec( import smtplib ) rJython$exec(from email.MIMEText import MIMEText) rJython$exec(import email.utils) mail-c( #Email settings fromaddr = 'ccqu...@gmail.com', toaddrs = 'userna...@somethinghere.com' - Show quoted text - jython.exec(rJython,mail) # and here is the error I get. Error in ls(envir = envir, all.names = private) : invalid 'envir' argument Just in case someone asks, I can do this: y = a test ...and the above email sends fine with 'a test' as the msg body. Any ideas? PS - I received lots of suggestions. Thank you very much for your effort/input. Ben On Mon, Aug 29, 2011 at 6:01 PM, Henrique Dallazuanna www...@gmail.com wrote: Try: paste(c(a, b, c), collapse = \n) On Mon, Aug 29, 2011 at 8:56 PM, Ben qant ccqu...@gmail.com wrote: Hello, Does anyone know how to convert this: msg [1] a [2] b [3] c To: msg a b c In other words, I need to convert a character vector to a single string with carriage returns for each row. Functionally, I'm attempting to send an email of a character vector in a way that is readable in the email body. I can only input one string as the message body parameter. I'm using rJython to send the email because I need authentication. Thanks! [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Henrique Dallazuanna Curitiba-Paraná-Brasil 25° 25' 40 S 49° 16' 22 O [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. David Winsemius, MD West Hartford, CT [[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] ATSP to TSP reformulation
Hi Ian, I checked your example again and found the problem in tsp. fix(x) seems to create column names but not row names which exposes a bug in as.ATSP in tsp. This code replicates your error message: library(TSP) x - rbind(c(1,2,3,4), c(1,0,11,5), c(2,4,0,6), c(3,5,6,0)) colnames(x) - 1:4 #rownames(x) - 1:4 atsp - ATSP(x) tsp - reformulate_ATSP_as_TSP(atsp) if you uncomment the rownames line then it works. I already fixed the code in tsp to check for missing col/row names in the matrix. This fix will be part of the next release. For now please just add row names to the matrix. Thanks for the bug report! -Michael -- Dr. Michael Hahsler, Visiting Assistant Professor Department of Computer Science and Engineering Lyle School of Engineering Southern Methodist University, Dallas, Texas (214) 768-8878 * mhahs...@lyle.smu.edu * http://lyle.smu.edu/~mhahsler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] rpart: apply tree to new data to get counts
Jay josip.2...@gmail.com het geskryf When I have made a decision tree with rpart, is it possible to apply this tree to a new set of data in order to find out the distribution of observations? Ideally I would like to plot my original tree, with the counts (at each node) of the new data. Sadly, neither plot.rpart or rpart.plot support plotting a tree trained on one set of data but showing results predicted for a new set of data. Page 21 of the vignette for the rpart.plot package has this to say Arguably the most serious limitation of the current implementation is its inability to display results on test data (on the tree derived from the training data). One way of implementing this (quite a lot of work) would be to extend the rpart function to include a newdata argument. If given such an argument, rpart would additionally return new.frame, new.where, and new.y fields (corresponding to the existing frame, where, and y fields). The plotting functions could then trivially be extended to use these new fields. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] locate the needed columns
Hi All, I have a data frame, whose colnames like A.x, B.x, C.x, A.y, B.y, C.y. There could be many columns like this pattern. I want to compare data in columns A.x with A.y, B.x with B.y and C.x with C.y etc. Suppose my data frame is d, names(d) = c(A.x, B.x, C.x, A.y, B.y, C.y); If I want to D1 = data.frame(d$A.x, d$A.y); D2 = data.frame(d$B.x, d$B.y); etc. or do other operation for each pair, What is elegant way to do it rather than use a loop? Thanks. HXD [[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] having trouble extracting week from chron object
Here it is with the output: library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts [1] 02/27/92 02/27/92 01/14/92 02/28/92 02/01/92 dts.chron - as.chron(dts) dts.chron [1] 02/27/92 02/27/92 01/14/92 02/28/92 02/01/92 class(dts.chron) [1] dates times # all of these component extractions work: months(dts.chron) [1] Feb Feb Jan Feb Feb 12 Levels: Jan Feb Mar Apr May Jun Jul Aug Sep ... Dec weekdays(dts.chron) [1] Thu Thu Tue Fri Sat Levels: Sun Mon Tue Wed Thu Fri Sat years(dts.chron) [1] 1992 1992 1992 1992 1992 Levels: 1992 quarters(dts.chron) [1] 1Q 1Q 1Q 1Q 1Q Levels: 1Q 2Q 3Q 4Q # but weeks() doesn't seem to work weeks(dts.chron) Error: could not find function weeks ?weeks No documentation for 'weeks' in specified packages and libraries: you could try '??weeks' weeks Error: object 'weeks' not found week Error: object 'week' not found sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] chron_2.3-42 Thanks. --Chris Ryan On Tue, Aug 30, 2011 at 1:54 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 30, 2011, at 1:36 PM, Christopher W Ryan wrote: Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts dts.chron - as.chron(dts) dts.chron class(dts.chron) # all of these component extractions work: months(dts.chron) weekdays(dts.chron) years(dts.chron) quarters(dts.chron) # but weeks() doesn't seem to work It doesn't work for me either but since I also have the package lubridate loaded, and ?weeks brings up a lubridate help page, I don't feel I have any right to complain. I get an error message what did you get?: Error in Ops.dates(pieces$week, 7) : * not defined for chron objects If I were posting I would also have had the good sense to include the output of sessionInfo(). weeks(dts.chron) Try type just: weeks # I get a lubridate function. ?chron tells me: Bur what does ?weeks tell you? . . . The functions days(), months(), quarters(), years(), weeks(), weekdays(), hours(), minutes(), and seconds() take any chron object as input and extract the corresponding time interval . . . . Any advice? Thanks. Chris Ryan SUNY Upstate Medical University Clinical Campus at Binghamton Binghamton, NY __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Why does loading saved/cached objects add significantly to RAM consumption?
Hi. On Tue, Aug 30, 2011 at 3:59 AM, Janko Thyson janko.thyson.rst...@googlemail.com wrote: Dear list, I make use of cached objects extensively for time consuming computations and yesterday I happened to notice some very strange behavior in that respect: When I execute a given computation whose result I'd like to cache (tried both saving it as '.Rdata' and via package 'R.cache' which uses a own filetype '.Rcache'), Just to clarify, it is just the filename extension that is custom; it uses base::save() internally. It is very unlikely that R.cache has to do with your problem. my R session consumes about 200 MB of RAM, which is fine. Now, when I make use of the previously cached object (i.e. loading it, assigning it to a certain field of a Reference Class object), I noticed that RAM consumption of my R process jumps to about 250 MB! a Each new loading of cached/saved objects adds to that consumption (in total, I have about 5-8 objects that are processed this way), so at some point I easily get a RAM consumption of over 2 GB where I'm only at about 200 MB of consumption when I compute each object directly! Object sizes (checked with 'object.size()') remain fairly constant. What's even stranger: after loading cached objects and removing them (either via 'rm()' or by assigning a 'fresh' empty object to the respective Reference Class field, RAM consumption remains at this high level and never comes down again. I checked the behavior also in a small example which is a simplification of my use case and which you'll find below (checked both on Win XP and Win 7 32 bit). I couldn't quite reproduce an immediate increase in RAM consumption, I couldn't reproduce it either using sessionInfo(): R version 2.13.1 Patched (2011-08-29 r56823) Platform: x86_64-pc-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] tools_2.13.1 but what I still find really strange is a) why do repeated 'load()' calls result in an increase in RAM consumption? b) why does the latter not go down again after the objects have been removed from '.GlobalEnv'? Removed objects may still sit in memory - it is only when R's garbage collector (GC) comes around and removes them that the memory usage goes down. You can force the garbage collector to run by calling gc(), but normally it is automatically triggered whenever needed. Note that the GC will only be able to clean up the memory of removed objects IFF there are no other references to that object/piece of memory. When you use References classes (cf. setRefClass()) and environments, you end up keeping references internally in objects without being aware of it. My guess is that your other code may have such issues, whereas the code below does not. There is also the concept of promises [see 'R Language Definition' document], which *may* also be involved. FYI, the Sysinternals Process Explorer [http://technet.microsoft.com/en-us/sysinternals/bb896653] is a useful tool for studying individual processes such as R. My $.02 Henrik Did anyone of you experience a similar behavior? Or even better, does anyone know why this is happening and how it might be fixed (or be worked around)? ;-) I really need your help on this one as it's crucial for my thesis, thanks a lot for anyone replying!! Regards, Janko # EXAMPLE # setRefClass(A, fields=list(.PRIMARY=environment)) setRefClass(Test, fields=list(a=A)) obj.1 - lapply(1:5000, function(x){ rnorm(x) }) names(obj.1) - paste(sample, 1:5000, sep=.) obj.1 - as.environment(obj.1) test - new(Test, a=new(A, .PRIMARY=obj.1)) test$a$.PRIMARY$sample.10 #+ object.size(test) object.size(test$a) object.size(obj.1) # RAM used by R session: 118 MB save(obj.1, file=C:/obj.1.Rdata) # Results in an object of ca. 94 MB save(test, file=C:/test.Rdata) # Results in an object of ca. 94 MB # START A NEW R SESSION # load(C:/test.Rdata) # RAM consumption still fine at 115 - 118 MB # But watch how it goes up as we repeatedly load objects for(x in 1:5){ load(C:/test.Rdata) } for(x in 1:5){ load(C:/obj.1.Rdata) } # Somehow there seems to be an upper limit, though # Removing the objects does not bring down RAM consumption rm(obj.1) rm(test) ## Sys.info() sysname release Windows XP version nodename build 2600, Service Pack 3 ASHB-109C-02 machine login x86 wwa418 user wwa418 sessionInfo() R version
Re: [R] Error in f(x, ...) : could not find function f2
On 30.08.2011 14:31, . . wrote: Hi all, I am getting the erro showed in the subject. I was strange the this becomes to happen after a computer restar. I think after the restart another function f2 was in memory and it scape from me. func- Vectorize(FUN= function(y, frac, rate, sad, samp=Poisson, trunc=0, ...){ f0- function(y,frac,n) { f1- function(y,frac,n){ dpois(y,frac*n) } dcom- paste(d,deparse(substitute(sad)),sep=) dots- c(as.name(n),list(...)) f2- call(dcom,dots) f- function(n){ f1(y,frac,n)*f2(n) } . ., obviously f2 is a call rather than a function. Uwe Ligges myintegrate- function() { r- 0 r1- 1 x1- 0 dx- 20 while(r1 10e-500) { r1- integrate(f,x1,x1+dx)$value r- r + r1 x1- x1 + dx } integrate(f,x1,Inf)$valu } myintegrate() } f0(y,frac,n)/(1-f0(trunc,frac,n)) },y) func(10, 0.1, 0.1, exp) Any idea? Thanks in advance. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ATSP to TSP reformulation
It worked fabulously. Thank you so much for help and time. -- View this message in context: http://r.789695.n4.nabble.com/ATSP-to-TSP-reformulation-tp3777105p3779476.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] column names with rbind loop
How about to add a conditional statement to get the header from 1st file for(i in all.files) { if (i==all.files[1]) new.data - read.table(i,header=TRUE) else { new.data - rbind(new.data, read.table(i))}} Weidong Gu On Tue, Aug 30, 2011 at 1:42 PM, Vining, Kelly kelly.vin...@oregonstate.edu wrote: Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this: all.files - list.files() all.files [1] 1.rpkm 10.rpkm 11.rpkm 12.rpkm 13.rpkm 14.rpkm [7] 15.rpkm 16.rpkm 17.rpkm 18.rpkm 19.rpkm 2.rpkm [13] 3.rpkm 4.rpkm 5.rpkm 6.rpkm 7.rpkm 8.rpkm [19] 9.rpkm Then loop through them like this: new.data - NULL for(i in all.files) { + in.data - read.table(i) + new.data - rbind(new.data, in.data)} head(new.data) V1 V2 V3 V4 V5 V6 V7 1 seq_id source type start end score strand 2 scaffold_1 Ptrichocarpav2_0 gene_body 12639 13384 . + 3 scaffold_1 Ptrichocarpav2_0 gene_body 22190 22516 . + 4 scaffold_1 Ptrichocarpav2_0 gene_body 74076 75893 . + 5 scaffold_1 Ptrichocarpav2_0 gene_body 80207 81289 . - 6 scaffold_1 Ptrichocarpav2_0 gene_body 105236 107712 . + As you can see, R is putting a V1, V2... header row here because I didn't say header=TRUE in my read.table command. But if I do this within the loop, I get an error. If I try to delete the V1, V2 row after the fact by new.data - new.data[-1,] R deletes my real header row. How can I get the header that I want? Thanks for any help, --Kelly V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Multiple Traveling Salesperson Problem
Hi Ian, There is currently no support for the mTSP in tsp. The paper Tolga Bektas, The multiple traveling salesman problem: an overview of formulations and solution procedures, Omega, 34(3), June 2006, Pages 209-219 describes some methods to reformulate a mTSP as a regular TSP. However, I had no time to look at those... -Michael -- Dr. Michael Hahsler, Visiting Assistant Professor Department of Computer Science and Engineering Lyle School of Engineering Southern Methodist University, Dallas, Texas (214) 768-8878 * mhahs...@lyle.smu.edu * http://lyle.smu.edu/~mhahsler __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] ROC plot for KNN
Hi I need some help with ploting the ROC for K-nearest neighbors. Since KNN is a non-parametric classification methods, the predicted value will be either 0 or 1. It will not be able to test for different cutoff to plot ROC. What is the package or functions I should use to plot ROC for KNN? Thanks. Qian [[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] splitting into multiple dataframes and then create a loop to work
Thank you for the help. My focus was to split data frame for a different function, not lm. I could provide detail of that lengthy function instead I provided the lm function. The comment were very helpful. Thanks; NIL On Mon, Aug 29, 2011 at 3:37 PM, Dimitris Rizopoulos d.rizopou...@erasmusmc.nl wrote: well, if a pooled estimate of the residual standard error is not desirable, then you just need to set argument 'pool' of lmList() to FALSE, e.g., mlis - lmList(yvar ~ . - clvar | clvar, data = df, pool = FALSE) summary(mlis) Best, Dimitris On 8/29/2011 9:20 PM, Dennis Murphy wrote: Hi: Dimitris' solution is appropriate, but it needs to be mentioned that the approach I offered earlier in this thread differs from the lmList() approach. lmList() uses a pooled measure of error MSE (which you can see at the bottom of the output from summary(mlis) ), whereas the plyr approach subdivides the data into distinct sub-data frames and analyzes them as separate entities. As a result, the residual MSEs will differ between the two approaches, which in turn affects the significance tests on the model coefficients. You need to decide which approach is better for your purposes. Cheers, Dennis On Mon, Aug 29, 2011 at 12:02 PM, Dimitris Rizopoulos d.rizopou...@erasmusmc.nl wrote: You can do this using function lmList() from package nlme, without having to split the data frames, e.g., library(nlme) mlis- lmList(yvar ~ . - clvar | clvar, data = df) mlis summary(mlis) I hope it helps. Best, Dimitris On 8/29/2011 5:37 PM, Nilaya Sharma wrote: Dear All Sorry for this simple question, I could not solve it by spending days. My data looks like this: # data set.seed(1234) clvar- c( rep(1, 10), rep(2, 10), rep(3, 10), rep(4, 10)) # I have 100 level for this factor var; yvar- rnorm(40, 10,6); var1- rnorm(40, 10,4); var2- rnorm(40, 10,4); var3- rnorm(40, 5, 2); var4- rnorm(40, 10, 3); var5- rnorm(40, 15, 8) # just example df- data.frame(clvar, yvar, var1, var2, var3, var4, var5) # manual splitting df1- subset(df, clvar == 1) df2- subset(df, clvar == 2) df3- subset(df, clvar == 3) df4- subset(df, clvar == 4) df5- subset(df, clvar == 5) # i tried to mechanize it * for(i in 1:5) { df[i]- subset(df, clvar == i) } I know it should not work as df[i] is single variable, do it did. But I could not find away to output multiple dataframes from this loop. My limited R knowledge, did not help at all ! * # working on each of variable, just trying simple function a- 3:8 out1- lapply(1:5, function(ind){ lm(df1$yvar ~ df1[, a[ind]]) }) p1- lapply(out1, function(m)summary(m)$**coefficients[,4][2]) p1- do.call(rbind, p1) My ultimate objective is to apply this function to all the dataframes created (i.e. df1, df2, df3, df4, df5) and create five corresponding p-value vectors (p1, p2, p3, p4, p5). Then output would be a matrix of clvar and correponding p values clvar var1 var2 var3 var4 var5 1 2 3 4 Please help me ! Thanks NIL [[alternative HTML version deleted]] __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/**posting-guide.htmlhttp://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/**biostatistiek/http://www.erasmusmc.nl/biostatistiek/ __** R-help@r-project.org mailing list https://stat.ethz.ch/mailman/**listinfo/r-helphttps://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/** posting-guide.html http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Dimitris Rizopoulos Assistant Professor Department of Biostatistics Erasmus University Medical Center Address: PO Box 2040, 3000 CA Rotterdam, the Netherlands Tel: +31/(0)10/7043478 Fax: +31/(0)10/7043014 Web: http://www.erasmusmc.nl/**biostatistiek/http://www.erasmusmc.nl/biostatistiek/ [[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] column names with rbind loop
Thanks much for your help! This almost works. However, now I am getting the following error: for(i in all.files) { + if (i==all.files[1]) new.data - read.table(i,header=TRUE) else { + new.data - rbind(new.data, read.table(i))}} Error in match.names(clabs, names(xi)) : names do not match previous names I am wondering if this is because R adds row numbers as a numerical column to the table of the first file it reads? From: Weidong Gu [anopheles...@gmail.com] Sent: Tuesday, August 30, 2011 12:00 PM To: Vining, Kelly Cc: r-help@r-project.org Subject: Re: [R] column names with rbind loop How about to add a conditional statement to get the header from 1st file for(i in all.files) { if (i==all.files[1]) new.data - read.table(i,header=TRUE) else { new.data - rbind(new.data, read.table(i))}} Weidong Gu On Tue, Aug 30, 2011 at 1:42 PM, Vining, Kelly kelly.vin...@oregonstate.edu wrote: Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this: all.files - list.files() all.files [1] 1.rpkm 10.rpkm 11.rpkm 12.rpkm 13.rpkm 14.rpkm [7] 15.rpkm 16.rpkm 17.rpkm 18.rpkm 19.rpkm 2.rpkm [13] 3.rpkm 4.rpkm 5.rpkm 6.rpkm 7.rpkm 8.rpkm [19] 9.rpkm Then loop through them like this: new.data - NULL for(i in all.files) { + in.data - read.table(i) + new.data - rbind(new.data, in.data)} head(new.data) V1 V2V3 V4 V5V6 V7 1 seq_id source type startend score strand 2 scaffold_1 Ptrichocarpav2_0 gene_body 12639 13384 . + 3 scaffold_1 Ptrichocarpav2_0 gene_body 22190 22516 . + 4 scaffold_1 Ptrichocarpav2_0 gene_body 74076 75893 . + 5 scaffold_1 Ptrichocarpav2_0 gene_body 80207 81289 . - 6 scaffold_1 Ptrichocarpav2_0 gene_body 105236 107712 . + As you can see, R is putting a V1, V2... header row here because I didn't say header=TRUE in my read.table command. But if I do this within the loop, I get an error. If I try to delete the V1, V2 row after the fact by new.data - new.data[-1,] R deletes my real header row. How can I get the header that I want? Thanks for any help, --Kelly V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] locate the needed columns
If the pattern is characterized by capital letters as your sample suggests. The following code may help df-list() names(d) = c(A.x, B.x, C.x, A.y, B.y, C.y) group.v-matrix(NA,nrow=3,ncol=2) ### you may need to modify nrow and ncol for (i in 1:3) { group.v[i,]-names(d)[grep(LETTERS[i],names(d))] df[i]-d[,names(d)%in% group.v[i]] } Weidong Gu On Tue, Aug 30, 2011 at 2:31 PM, Hui Du hui...@dataventures.com wrote: Hi All, I have a data frame, whose colnames like A.x, B.x, C.x, A.y, B.y, C.y. There could be many columns like this pattern. I want to compare data in columns A.x with A.y, B.x with B.y and C.x with C.y etc. Suppose my data frame is d, names(d) = c(A.x, B.x, C.x, A.y, B.y, C.y); If I want to D1 = data.frame(d$A.x, d$A.y); D2 = data.frame(d$B.x, d$B.y); etc. or do other operation for each pair, What is elegant way to do it rather than use a loop? Thanks. HXD [[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] gradient function in OPTIMX
Hi, In my package CatDyn, which uses optimx, I included the gradients of 20 version of the model involved. I estimate model parameters with numerical gradients, and at the final estimates I calculate the analytical gradients. In the simplest version of the model the analytical gradients computed post hoc are almost identical to the numerical gradients. This shows that the analytical gradients (whose formulas were obtained by the CAS Maxima) are correct, at least for those simple versions of my model. However, if I try to pass the analytical gradients to optimx in a new optimization, I invariably get the error message that you got: Gradient function might be wrong - check it! This happens regardless of the method used (BFGS, spg, Rcgmin). Same as you, when I try to pass the gradients to optim, instead of optimx, the gradients are accepted and computed correctly, but then I cann't use the very nice other features of optimx. I wanted to report this to Ravi and Prof. Nash but I haven't got the time for a full report with several examples and variations. So now that you report it, here I am, seconding you in calling the attention to this apparent problem in optimx. Rubén H. Roa-Ureta, Ph. D. AZTI Tecnalia, Txatxarramendi Ugartea z/g, Sukarrieta, Bizkaia, SPAIN -Original Message- From: r-help-boun...@r-project.org on behalf of Kathie Sent: Mon 8/29/2011 11:10 AM To: r-help@r-project.org Subject: [R] gradient function in OPTIMX Dear R users When I use OPTIM with BFGS, I've got a significant result without an error message. However, when I use OPTIMX with BFGS( or spg), I've got the following an error message. optimx(par=theta0, fn=obj.fy, gr=gr.fy, method=BFGS, control=list(maxit=1)) Error: Gradient function might be wrong - check it! I checked and checked my gradient function line by line. I could not find anything wrong. Is it a bug or something? I prefer OPTIMX, so I'd like to know why. Thanks a lot in advance Regards, Kathryn Lord -- View this message in context: http://r.789695.n4.nabble.com/gradient-function-in-OPTIMX-tp3775791p3775791.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] Fwd: help with by command
Thanks very much for the help. I ended up getting it to work with one small change: by(foo, foo$V2, function(foo) mean(foo$trust, na.rm=T)) thanks again, Ari -- View this message in context: http://r.789695.n4.nabble.com/help-with-by-command-tp3766285p3779622.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] Generating a sequence of diagonal matrices
I am trying to generate a sequence of diagonal matrices. In the scalar case I would use something like, seq(0,100,by=1). How do I generalise the above for , say a 2 dimensional diagonal matrix. In other words how do I produce the series of diagonal matrices { diag(0,2),diag(1,2), diag(2,2),...,diag(100,2)}? Thanks Meddee -- View this message in context: http://r.789695.n4.nabble.com/Generating-a-sequence-of-diagonal-matrices-tp3779623p3779623.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] column names with rbind loop
On Aug 30, 2011, at 3:46 PM, Vining, Kelly wrote: Thanks much for your help! This almost works. However, now I am getting the following error: for(i in all.files) { + if (i==all.files[1]) new.data - read.table(i,header=TRUE) else { + new.data - rbind(new.data, read.table(i))}} Error in match.names(clabs, names(xi)) : names do not match previous names You need to decide if you are going to use the V-names or the original names because rbind requires that the names for its two arguments match. Perhaps you want to read the names in separately with readLines? Also look at the skip argument to read.tables. I am wondering if this is because R adds row numbers as a numerical column to the table of the first file it reads? It does so by default. It needs to have some sort of character vector to use, so if there is none, it makes up names. I don't understand why you didn't use, ... header =TRUE, for both read operations. -- David. From: Weidong Gu [anopheles...@gmail.com] Sent: Tuesday, August 30, 2011 12:00 PM To: Vining, Kelly Cc: r-help@r-project.org Subject: Re: [R] column names with rbind loop How about to add a conditional statement to get the header from 1st file for(i in all.files) { if (i==all.files[1]) new.data - read.table(i,header=TRUE) else { new.data - rbind(new.data, read.table(i))}} Weidong Gu On Tue, Aug 30, 2011 at 1:42 PM, Vining, Kelly kelly.vin...@oregonstate.edu wrote: Hello R users. This is a fairly basic question: I am concatenating data from sets of files in a directory using a loop. The column names in all files are exactly the same. My understanding is that rbind takes column names from the first file it reads. However, my output is showing that the column names are treated as a first data row, not treated as headers. I compile my file names like this: all.files - list.files() all.files [1] 1.rpkm 10.rpkm 11.rpkm 12.rpkm 13.rpkm 14.rpkm [7] 15.rpkm 16.rpkm 17.rpkm 18.rpkm 19.rpkm 2.rpkm [13] 3.rpkm 4.rpkm 5.rpkm 6.rpkm 7.rpkm 8.rpkm [19] 9.rpkm Then loop through them like this: new.data - NULL for(i in all.files) { + in.data - read.table(i) + new.data - rbind(new.data, in.data)} head(new.data) V1 V2V3 V4 V5V6 V7 1 seq_id source type startend score strand 2 scaffold_1 Ptrichocarpav2_0 gene_body 12639 13384 . + 3 scaffold_1 Ptrichocarpav2_0 gene_body 22190 22516 . + 4 scaffold_1 Ptrichocarpav2_0 gene_body 74076 75893 . + 5 scaffold_1 Ptrichocarpav2_0 gene_body 80207 81289 . - 6 scaffold_1 Ptrichocarpav2_0 gene_body 105236 107712 . + As you can see, R is putting a V1, V2... header row here because I didn't say header=TRUE in my read.table command. But if I do this within the loop, I get an error. If I try to delete the V1, V2 row after the fact by new.data - new.data[-1,] R deletes my real header row. How can I get the header that I want? Thanks for any help, --Kelly V. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. 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] RPostgreSQL Loading Issues
On Tue, 30 Aug 2011, Joe Conway wrote: Just a guess, but possibly because libpq.so (the postgres client library) is not being found. Joe, My initial thought, too. But, that's not it. 1) Do you have libpq.so installed on your system? 2) If so, where? 3) If it is not in a standard system location (e.g. /usr/lib), try adding an entry either to /etc/ld.so.conf or a file with the appropriate entry in /etc/ld.so.conf.d/ and then run ldconfig /usr/local/pgsql/lib/libpq.so /usr/local/pgsql/lib/libpq.so.5 /usr/local/pgsql/lib/libpq.so.5.3 /usr/lib/libpq.so /usr/lib/libpq.so.5 The softlinks in /usr/lib/ are to /usr/local/pgsql/lib/libpq.so.5.3. Since postgres-9.0.4 runs quite well here there must be some other factor in play. Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Generating a sequence of diagonal matrices
Hi Meddee, Try this: dmat - lapply(1:100, function(d) diag(d, 2)) That will give you a list of all 100 matrices. Cheers, Josh On Tue, Aug 30, 2011 at 1:00 PM, meddee meddee1...@gmail.com wrote: I am trying to generate a sequence of diagonal matrices. In the scalar case I would use something like, seq(0,100,by=1). How do I generalise the above for , say a 2 dimensional diagonal matrix. In other words how do I produce the series of diagonal matrices { diag(0,2),diag(1,2), diag(2,2),...,diag(100,2)}? Thanks Meddee -- View this message in context: http://r.789695.n4.nabble.com/Generating-a-sequence-of-diagonal-matrices-tp3779623p3779623.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 Programmer Analyst II, ATS Statistical Consulting Group University of California, Los Angeles https://joshuawiley.com/ __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] having trouble extracting week from chron object
You did read jannis' reply didn't you? -- David. On Aug 30, 2011, at 2:34 PM, Christopher W Ryan wrote: Here it is with the output: library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts [1] 02/27/92 02/27/92 01/14/92 02/28/92 02/01/92 dts.chron - as.chron(dts) dts.chron [1] 02/27/92 02/27/92 01/14/92 02/28/92 02/01/92 class(dts.chron) [1] dates times # all of these component extractions work: months(dts.chron) [1] Feb Feb Jan Feb Feb 12 Levels: Jan Feb Mar Apr May Jun Jul Aug Sep ... Dec weekdays(dts.chron) [1] Thu Thu Tue Fri Sat Levels: Sun Mon Tue Wed Thu Fri Sat years(dts.chron) [1] 1992 1992 1992 1992 1992 Levels: 1992 quarters(dts.chron) [1] 1Q 1Q 1Q 1Q 1Q Levels: 1Q 2Q 3Q 4Q # but weeks() doesn't seem to work weeks(dts.chron) Error: could not find function weeks ?weeks No documentation for 'weeks' in specified packages and libraries: you could try '??weeks' weeks Error: object 'weeks' not found week Error: object 'week' not found sessionInfo() R version 2.13.1 (2011-07-08) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] chron_2.3-42 Thanks. --Chris Ryan On Tue, Aug 30, 2011 at 1:54 PM, David Winsemius dwinsem...@comcast.net wrote: On Aug 30, 2011, at 1:36 PM, Christopher W Ryan wrote: Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) dts dts.chron - as.chron(dts) dts.chron class(dts.chron) # all of these component extractions work: months(dts.chron) weekdays(dts.chron) years(dts.chron) quarters(dts.chron) # but weeks() doesn't seem to work It doesn't work for me either but since I also have the package lubridate loaded, and ?weeks brings up a lubridate help page, I don't feel I have any right to complain. I get an error message what did you get?: Error in Ops.dates(pieces$week, 7) : * not defined for chron objects If I were posting I would also have had the good sense to include the output of sessionInfo(). weeks(dts.chron) Try type just: weeks # I get a lubridate function. ?chron tells me: Bur what does ?weeks tell you? . . . The functions days(), months(), quarters(), years(), weeks(), weekdays(), hours(), minutes(), and seconds() take any chron object as input and extract the corresponding time interval . . . . Any advice? Thanks. Chris Ryan SUNY Upstate Medical University Clinical Campus at Binghamton Binghamton, NY __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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. 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] having trouble extracting week from chron object
On Tue, Aug 30, 2011 at 1:36 PM, Christopher W Ryan cr...@binghamton.edu wrote: Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) Try this: as.numeric(cut(dts, weeks)) -- 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] RPostgreSQL Loading Issues
On 08/30/2011 10:53 AM, Rich Shepard wrote: Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared object '/home/rshepard/R/i486-slackware-linux-gnu-library/2.13/RPostgreSQL/libs/RPostgreSQL.so': libR.so: cannot open shared object file: No such file or directory Error: package/namespace load failed for 'RPostgreSQL' The shared library, of course, is present: [rshepard@salmo ~/R/i486-slackware-linux-gnu-library/2.13/RPostgreSQL/libs]$ ll -rwxr-xr-x 1 rshepard users 44385 2011-08-03 20:13 RPostgreSQL.so* Can someone explain to me what's going on and how I fix it? Just a guess, but possibly because libpq.so (the postgres client library) is not being found. 1) Do you have libpq.so installed on your system? 2) If so, where? 3) If it is not in a standard system location (e.g. /usr/lib), try adding an entry either to /etc/ld.so.conf or a file with the appropriate entry in /etc/ld.so.conf.d/ and then run ldconfig HTH, Joe -- Joe Conway credativ LLC: http://www.credativ.us Linux, PostgreSQL, and general Open Source Training, Service, Consulting, 24x7 Support __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] having trouble extracting week from chron object
On Tue, Aug 30, 2011 at 4:43 PM, Gabor Grothendieck ggrothendi...@gmail.com wrote: On Tue, Aug 30, 2011 at 1:36 PM, Christopher W Ryan cr...@binghamton.edu wrote: Running R 2.13.1 on Windows XP. I would like to get week of the year (1-52) for each date. library(chron) dts - dates(c(02/27/92, 02/27/92, 01/14/92,02/28/92, 02/01/92)) Try this: as.numeric(cut(dts, weeks)) although that won't label the weeks from the beginning of the year but rather the earliest date will be labelled week 1 so you need to add a date in the first of the year if you want that. Alternately try this: as.numeric(format(as.Date(dts), %w)) or use %W. See ?strptime for details. -- 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.
[R] Fwd: ARMA show different result between eview and R
-- Forwarded message -- From: John C Frain fra...@gmail.com Date: 30 August 2011 21:52 Subject: Re: [R] ARMA show different result between eview and R To: Young Gyu Park ygpa...@gmail.com If you check your manuals you will find that R uses full maximum likelihood while Eviews uses an alternative non-linear method. Many programs use different versions of information criteria but these are monotone transformations (ie they all have an extreme value with the same model. Again you need to check your manuals. Best Regards John On 30 August 2011 08:21, Young Gyu Park ygpa...@gmail.com wrote: When I do ARMA(2,2) using one lag of LCPIH data This is eview result *Dependent Variable: DLCPIH **Method: Least Squares **Date: 08/12/11 Time: 12:44 **Sample (adjusted): 1970Q2 2010Q2 **Included observations: 161 after adjustments **Convergence achieved after 14 iterations **MA Backcast: 1969Q4 1970Q1 ** **Variable Coefficient Std. Error t-Statistic Prob. ** **C 0.003361 0.001814 1.853352 0.0657 **DLCPIH(-1) -0.100150 0.053160 -1.883917 0.0614 **DLCPIH(-2) 0.870456 0.052466 16.59075 0. **MA(1) 0.532252 0.100110 5.316678 0. **MA(2) -0.379383 0.099535 -3.811566 0.0002 ** **R-squared 0.512067 Mean dependent var 0.014816 **Adjusted R-squared 0.499556 S.D. dependent var 0.016274 **S.E. of regression 0.011513 Akaike info criterion -6.060182 **Sum squared resid 0.020676 Schwarz criterion -5.964486 **Log likelihood 492.8446 Hannan-Quinn criter. -6.021326 **F-statistic 40.92897 Durbin-Watson stat 2.012062 **Prob(F-statistic) 0.00 ** **Inverted MA Roots .40 -.94 * This is R result * dlcpihTsLen - length(ausT2Ts[,4]) ** dlcpihArma22Fit - arima(ausT2Ts[,4], order=c(2,1,2), xreg=1:dlcpihTsLen) ** dlcpiArma22hFit - arima(ausT2Ts[,4], order=c(2,1,2)) ** dlcpihArma22Fit * *Call: **arima(x = ausT2Ts[, 4], order = c(2, 1, 2), xreg = 1:dlcpihTsLen) * *Coefficients: ** ar1 ar2 ma1 ma2 1:dlcpihTsLen ** -0.1083 0.8673 0.5263 -0.3716 0.0146 **s.e. 0.0493 0.0484 0.0894 0.0852 0.0041 * *sigma^2 estimated as 0.0001282: log likelihood = 498.38, aic = -984.76* * * * * I wonder why the coefficient values are little bit different between them. * * Another thing I wonder is why the AIC value is so significantly different each other*.* * * Please help me, if anyone who have experience both of eview and R is in R community. 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. -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com -- John C Frain Economics Department Trinity College Dublin Dublin 2 Ireland www.tcd.ie/Economics/staff/frainj/home.html mailto:fra...@tcd.ie mailto:fra...@gmail.com __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Descriptive Stats from Data Frame
I don't find how to do what I need to do in Dalgaard or 'R Cookbook', so I'm asking here. I have a data frame with water chemistry data and I want to start exploring these data. There are three factors (site, date, chemical) associated with each measurement. The data frame looks like this: summary(chemdata) site_id.sample_date.param.quant BC-0.5|1996-04-19|Arsenic|0.01 :1 BC-0.5|1996-04-19|Calcium|76.56 :1 BC-0.5|1996-04-19|Chloride|12 :1 BC-0.5|1996-04-19|Magnesium|43.23 :1 BC-0.5|1996-04-19|Sulfate|175 :1 BC-0.5|1996-04-19|Total Dissolved Solids|460:1 (Other) :14880 I want first to calculate (and plot) descriptive stats by chemical, ignoring site and date and telling R to ignore missing data. (Incorporating those factors will occur later.) What I have not been able to figure out is how to specify the command to, for example, calculate mean and sd for Arsenic. My floundering and thrashing includes attempts like these: mean(chemdata.param=Arsenic) Error in is.numeric(x) : 'x' is missing mean(chemdata.quant, param=Arsenic) Error in mean(chemdata.quant, param = Arsenic) : object 'chemdata.quant' not found mean(chemdata$quant, param=Arsenic) [1] NA Warning message: In mean.default(chemdata$quant, param = Arsenic) : argument is not numeric or logical: returning NA As a newcomer to R I've done a lot of reading, yet all the examples use nicely structured data to illustrate the point being made. I need to work with my data and learn how to specify columns and write correct commands for the analyses I need. Please point me in the right direction. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
Hi Rich, It is a bit hard to read the summary you are using. Consider please pasting the output of: ls.str(chemdata) Regarding your question, please start and see if this work (I'm not sure, since it seems you have made some changes to the summary output, and I am only guessing how things look): mean(chemdata$quant[chemdata$param ==Arsenic]) sd(chemdata$quant[chemdata$param ==Arsenic]) Cheers, Tal Contact Details:--- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) -- On Wed, Aug 31, 2011 at 12:00 AM, Rich Shepard rshep...@appl-ecosys.comwrote: mean(chemdata.param=Arsenic) [[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] Descriptive Stats from Data Frame
On Aug 30, 2011, at 5:00 PM, Rich Shepard wrote: I don't find how to do what I need to do in Dalgaard or 'R Cookbook', so I'm asking here. I have a data frame with water chemistry data and I want to start exploring these data. There are three factors (site, date, chemical) associated with each measurement. The data frame looks like this: summary(chemdata) site_id.sample_date.param.quant It appears that your original file was delimited by | and your used something else, perhaps the default white-space setting? I think you need to go back and do your input operations again with sep=| (Or you could provide str() on the data.frame rather than making us guess.) -- David BC-0.5|1996-04-19|Arsenic|0.01 :1 BC-0.5|1996-04-19|Calcium|76.56 :1 BC-0.5|1996-04-19|Chloride|12 :1 BC-0.5|1996-04-19|Magnesium|43.23 :1 BC-0.5|1996-04-19|Sulfate|175 :1 BC-0.5|1996-04-19|Total Dissolved Solids|460:1 (Other) :14880 I want first to calculate (and plot) descriptive stats by chemical, ignoring site and date and telling R to ignore missing data. (Incorporating those factors will occur later.) What I have not been able to figure out is how to specify the command to, for example, calculate mean and sd for Arsenic. My floundering and thrashing includes attempts like these: mean(chemdata.param=Arsenic) Error in is.numeric(x) : 'x' is missing mean(chemdata.quant, param=Arsenic) Error in mean(chemdata.quant, param = Arsenic) : object 'chemdata.quant' not found mean(chemdata$quant, param=Arsenic) [1] NA Warning message: In mean.default(chemdata$quant, param = Arsenic) : argument is not numeric or logical: returning NA As a newcomer to R I've done a lot of reading, yet all the examples use nicely structured data to illustrate the point being made. I need to work with my data and learn how to specify columns and write correct commands for the analyses I need. Please point me in the right direction. Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
On Wed, 31 Aug 2011, Tal Galili wrote: It is a bit hard to read the summary you are using. Consider please pasting the output of: ls.str(chemdata) Tal, Yes, summary() is inappropriate. I do want str() instead. And what that shows is: str(chemdata) 'data.frame': 14886 obs. of 1 variable: $ site_id.sample_date.param.quant: Factor w/ 14886 levels BC-0.5|1996-04-19|Arsenic|0.01,..: 11579 14219 13298 11982 11909 13371 13082 111 12 23 ... Regarding your question, please start and see if this work (I'm not sure, since it seems you have made some changes to the summary output, and I am only guessing how things look): mean(chemdata$quant[chemdata$param ==Arsenic]) mean(chemdata$quant[chemdata$param ==Arsenic]) Error: unexpected '==' in mean(chemdata$quant[chemdata$param == mean(chemdata$quant[chemdata$param ==Arsenic]) [1] NA Warning message: In mean.default(chemdata$quant[chemdata$param == Arsenic]) : argument is not numeric or logical: returning NA I find it easy following the syntax in the half-dozen or more books I've read, but quite difficult to apply what I read to my own real-world data. :-) Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
On Tue, 30 Aug 2011, David Winsemius wrote: It appears that your original file was delimited by | and your used something else, perhaps the default white-space setting? David, Yes, the csv file separator is the pipe. I think you need to go back and do your input operations again with sep=| (Or you could provide str() on the data.frame rather than making us guess.) str(chemdata) 'data.frame': 14886 obs. of 1 variable: $ site_id.sample_date.param.quant: Factor w/ 14886 levels BC-0.5|1996-04-19|Arsenic|0.01,..: 11579 14219 13298 11982 11909 13371 13082 111 12 23 ... Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
On Aug 30, 2011, at 5:30 PM, Rich Shepard wrote: On Tue, 30 Aug 2011, David Winsemius wrote: It appears that your original file was delimited by | and your used something else, perhaps the default white-space setting? David, Yes, the csv file separator is the pipe. It is _not_ a csv file. You need to use read.table with sep = |. I think you need to go back and do your input operations again with sep=| (Or you could provide str() on the data.frame rather than making us guess.) str(chemdata) 'data.frame': 14886 obs. of 1 variable: $ site_id.sample_date.param.quant: Factor w/ 14886 levels BC-0.5|1996-04-19|Arsenic|0.01,..: 11579 14219 13298 11982 11909 13371 13082 111 12 23 ... Thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
On Tue, 30 Aug 2011, David Winsemius wrote: I think you need to go back and do your input operations again with sep=| David, Yes, that's better. I did not know of the sep option. The new results: str(chemdata) 'data.frame': 14886 obs. of 4 variables: $ site_id: Factor w/ 148 levels BC-0.5,BC-1,..: 104 145 126 115 114 128 124 2 3 3 ... $ sample_date: Factor w/ 1012 levels 1980-03-01,1980-05-01,..: 432 410 423 405 398 408 401 360 366 407 ... $ param : Factor w/ 8 levels Arsenic,Calcium,..: 1 1 1 1 1 1 1 1 1 1 ... $ quant : num 0.06 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 ... Now I can work on the commands I need. Many thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] Descriptive Stats from Data Frame
On Aug 30, 2011, at 5:38 PM, Rich Shepard wrote: On Tue, 30 Aug 2011, David Winsemius wrote: I think you need to go back and do your input operations again with sep=| David, Yes, that's better. I did not know of the sep option. The new results: str(chemdata) 'data.frame': 14886 obs. of 4 variables: $ site_id: Factor w/ 148 levels BC-0.5,BC-1,..: 104 145 126 115 114 128 124 2 3 3 ... $ sample_date: Factor w/ 1012 levels 1980-03-01,1980-05-01,..: 432 410 423 405 398 408 401 360 366 407 ... $ param : Factor w/ 8 levels Arsenic,Calcium,..: 1 1 1 1 1 1 1 1 1 1 ... $ quant : num 0.06 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 ... Now I can work on the commands I need. That does look more workable. You might consider changing the dates with: chemadata$samp_date - as.Date(as.character(chemdata$sample_date) ) Many thanks, Rich __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/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] putting in special characters in print statements
Dear R People: Here is a question which probably has a very simple answer. I want to print \end{verbatim} in the output of a sink file. If I put in \end{verbatim} I get an unrecognized escape sequence. If I put in \\end{verbatim}, it runs fine, but the output is \\end{verbatim} How do I get just one bracket, please? Thanks, Erin -- Erin Hodgess Associate Professor Department of Computer and Mathematical Sciences University of Houston - Downtown mailto: erinm.hodg...@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.