Re: [R] what constitutes a 'complete sentence'?
On 07 Jul 2015, at 16:52 , Max Kuhn mxk...@gmail.com wrote: What are we trying to fix? Two things, actually. (1) An error message that sends the package developer on a wild goose chase, because it is both out of sync both with what is wanted, and what is checked for. (2) The description in the WRE manual is somewhat self-contradicting, and could probably be improved. To my mind, the tricky one is (1). (2) should be easier because there is space to elaborate. (1) needs to be succinct, which is hard if there is no single term for what is being required. I'm beginning to think that the best we can do is along the lines of Malformed Description field: Missing end punctuation.. If more checks are devised, add more messages. -- Peter Dalgaard, Professor, Center for Statistics, Copenhagen Business School Solbjerg Plads 3, 2000 Frederiksberg, Denmark Phone: (+45)38153501 Office: A 4.23 Email: pd@cbs.dk Priv: pda...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] valid LRT between MASS::polr and nnet::multinom
Dear Steve, The short answer is no, but the test you propose is in my experience usually a close approximation to a valid test. The proportional-odds and multinomial-logistic regression models differ in two ways: the po model has an equal-coefficients (parallel-regressions) assumptions (except for intercepts) and so has fewer parameters; the po model models cumulative logits, while the mnl model models individual-category logits. As a consequence of the latter difference, the po model is not a specialization of the mnl model, as required by the LR test. A proper test of the po (equal-coefficients) assumption is to fit a cumulative-logit model with this constraint. You can do this with the vglm() function in the VGAM package using the cumulative family. Here is an example: -- snip - library(effects) # for WVS data library(nnet) # for multinom() library(MASS) # for polr() library(VGAM) # for vglm() Loading required package: stats4 Loading required package: splines mod.polr - polr(poverty ~ gender + religion + degree + country*poly(age,3), +data=WVS) coef(mod.polr) gendermale religionyes degreeyes 0.1691953 0.1684846 0.1413380 countryNorway countrySweden countryUSA -0.3217821 -0.5732783 0.6040006 poly(age, 3)1 poly(age, 3)2 poly(age, 3)3 19.9101983 -10.2208416 6.1157062 countryNorway:poly(age, 3)1 countrySweden:poly(age, 3)1countryUSA:poly(age, 3)1 -17.0042706 -9.4160841 1.5577738 countryNorway:poly(age, 3)2 countrySweden:poly(age, 3)2countryUSA:poly(age, 3)2 17.3824147 17.3856575 10.1575695 countryNorway:poly(age, 3)3 countrySweden:poly(age, 3)3countryUSA:poly(age, 3)3 3.5181428 2.3652443 -8.4004861 logLik(mod.polr) 'log Lik.' -5182.602 (df=20) mod.vglm.p - vgam(poverty ~ gender + religion + degree + country*poly(age,3), +data=WVS, family=cumulative(parallel=TRUE)) coef(mod.vglm.p) # same within rounding as polr except for sign (Intercept):1 (Intercept):2 gendermale 0.2139034 2.0267774 -0.1691716 religionyes degreeyes countryNorway -0.1684541 -0.1413316 0.3218158 countrySweden countryUSA poly(age, 3)1 0.5733987 -0.6040348 -19.9340368 poly(age, 3)2 poly(age, 3)3 countryNorway:poly(age, 3)1 10.2120529 -6.1558215 17.0535729 countrySweden:poly(age, 3)1countryUSA:poly(age, 3)1 countryNorway:poly(age, 3)2 9.4712722 -1.5238183 -17.3344400 countrySweden:poly(age, 3)2countryUSA:poly(age, 3)2 countryNorway:poly(age, 3)3 -17.3422095 -10.1469673 -3.4087977 countrySweden:poly(age, 3)3countryUSA:poly(age, 3)3 -2.2649306 8.4423869 logLik(mod.vglm.p) # same (within rounding error) [1] -5182.601 mod.multinom - multinom(poverty ~ gender + religion + degree + country*poly(age,3), + data=WVS) # weights: 60 (38 variable) initial value 5911.632725 iter 10 value 5162.749080 iter 20 value 5007.247684 iter 30 value 4995.375350 iter 40 value 4989.909216 iter 50 value 4987.650806 iter 60 value 4987.190310 iter 70 value 4987.131548 iter 80 value 4987.075422 final value 4987.073531 converged logLik(mod.multinom) 'log Lik.' -4987.074 (df=38) length(coef(mod.multinom)) [1] 38 mod.vglm.np - vgam(poverty ~ gender + religion + degree + country*poly(age,3), +data=WVS, family=cumulative(parallel=FALSE)) logLik(mod.vglm.np) # close but not the same as multinom [1] -4988.865 length(coef(mod.vglm.np)) # same no. of coefs [1] 38 snip -- Best, John John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.mcmaster.ca/jfox/ On Wed, 8 Jul 2015 04:18:58 + Steve Taylor steve.tay...@aut.ac.nz wrote: Dear R-helpers, Does anyone know if the likelihoods calculated by these two packages are comparable in this way? That is, is this a valid likelihood ratio test? # Reproducable example: library(MASS) library(nnet) data(housing) polr1 =
[R] R-project on App-V 5
Hi Here at Aberdeen Asset Management . We are in the process of looking to move to a VDI environment (based on Win7) and are wanting to deploy the R-project via Microsoft App-V 5. Based around this I have a series of technical queries regarding your application. Firstly can I ask you to please provide me (or point me towards a download location) the current version of software, including an installation guide, and any updates / patches needed? The company that is packaging our applications into the App-V environment have asked us the following questions (feel free to point me to the install guide where applicable on these queries): - are there any pre-requisites (such as Java for instance) or dependant applications? - is the app 32-bit or 64-bit? - is there any 16-bit code in the app? - is it compatible with Win7 64 bit?. - does is support RDSH (64bit XenApp 7.6) - does it support App-V 5? - any other vendor technical support contact. - how are updates managed and what is their typical frequency? - Are there licensing details regarding the product, and if so please advise on how it is controlled / locked down. Please come back to me with any questions you may have on my requests, otherwise thanks in advance for the assistance. Regards Gilfred Tan Discovery Engineer Aberdeen Asset Management Asia Limited (Reg. No. 199105448E) Tel: +65 6395 2642 aberdeen-asset.comhttp://www.aberdeen-asset.com/ Find out how aspects of everyday life embody our philosophy at Aberdeen simplyaberdeen.comhttp://www.simplyaberdeen.com This email and any attachment are confidential and may contain privileged and copyright information. It is intended solely for the addressee. If you are not the intended recipient, please notify the sender immediately and delete this email. In accordance with good business practice and applicable regulations, all electronic communications with the Aberdeen Asset Management Group of companies may be monitored and retained. Aberdeen Asset Management PLC, Company Number: SC82015, Registered Office: Ten Queen's Terrace, Aberdeen AB10 1YG Scotland. For further information please visit our website: http://www.aberdeen-asset.com and www.aberdeen-asset.com/aam.nsf/AAM/privacy. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 graphs with a single legend and trellis graph
Hi Rosa, As you are using base graphics, here is an example that might be of use. As we don't have access to your data, I have used something similar to the toy data in the example for the panes function. This could be done better using the split.screen function, so let me know if you would like an example using that. library(plotrix) # start a wide plotting device x11(width=10,height=4) y-runif(100) oldpar-panes(matrix(1:6,nrow=2,byrow=TRUE),widths=c(1,1,1.7)) par(mar=c(0,2,1.8,0)) boxplot(y,axes=FALSE) axis(2) box() par(mar=c(0,0,1.8,0)) tab.title(Boxplot of y,tab.col=#88dd88,cex=1) y_hist-hist(y,axes=FALSE,breaks=seq(0,1,length.out=5)) box() tab.title(Histogram of y,tab.col=#dd8800,cex=1) par(mar=c(0,0,1.8,12)) pie(y_hist$counts,col=2:9) tab.title(Pie chart of y categories,tab.col=#dd,cex=1) box() par(mar=c(2,2,1.8,0)) plot(y,xaxs=i,xlim=c(0,101),axes=FALSE,col=2:9) axis(2) box() tab.title(Scatterplot of y,tab.col=#aabbcc,cex=1) par(mar=c(2,0,1.8,0)) plot(sort(y),xaxs=i,xlim=c(0,101),axes=FALSE,col=2:9) box() tab.title(Scatterplot of y sorted,tab.col=#ddbc44,cex=1) # center the title at the middle of the fifth plot mtext(Overall title of plot,side=1,line=0.8,cex=1.5) par(mar=c(2,0,1.8,12)) plot(diff(y),xaxs=i,xlim=c(0,100),axes=FALSE,col=2:9) axis(4) box() tab.title(Scatterplot of diff(y),tab.col=#ff33cc,cex=1) legend(115,1.8, c(Boxplot,Histogram,Pie chart,Scatterplot,Sort,Diff), fill=c(#88dd88,#dd8800,#dd,#aabbcc,#ddbc44,#ff33cc), xpd=NA) Jim On Wed, Jul 8, 2015 at 1:05 PM, David Winsemius dwinsem...@comcast.net wrote: On Jul 7, 2015, at 2:45 PM, Rosa Oliveira wrote: Iam trying to plot 6 graphs in one single plot and I was able to, nonetheless I wanted that all graphs had just 1 common legend, as the legend is the same for all the 6 graphs and there is no sense in repeating it 6 times and even more, the legends in each graph sometimes don’t fit the graph. Is there a way to put just one legend for all the 6 graphs ate the same time? I was told to use a trellis graph, but after days of trying to do that I wasn’t able to. Can anyone help me? library(ggplot2) library(reshape) library(lattice) Why did you load those packages above? As far as I can see you did not use any lattice or ggplot2 functions. (Also see no reshape or reshape2 functions in use.) par(mfrow=c(2,3)) mse.alpha1 -read.csv(file=graphs_mse_alpha1.csv,head=TRUE,sep=,) And there you lose us. We are unable to see your data. The `legend` function can put the legend anywhere. You may need to set par(xpd=TRUE) if the location is outside the current plot area. If you wnated just one legend then you mus ask yourself why you are issuing multiple legend calls. I see the token-`legend` a total of 12 times in the code below. attach(mse.alpha1) names(mse1000.alpha1) mse.alpha2 -read.csv(file=graphs_mse_alpha2.csv,head=TRUE,sep=,) attach(mse.alpha2) names(mse.alpha2) nsample==50 plot(mse.alpha1$lambda[mse.alpha1$nsample==50], mse.alpha1$mse.naive[mse.alpha1$nsample==50], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 ) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.RegCal[mse.alpha1$nsample==50],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.PL[mse.alpha1$nsample==50],col=3,lty=3) title ( expression (paste (Mean squared error for , alpha[1])), cex.main=1.5) title(\n\n sample size=50) legend(.7,1, legend= c(Naive, Regression Calibration, Pseudo Likelihood), bty = n,col=c(4,2,3),lty=c(4,2,3)) plot(mse.alpha1$lambda[mse.alpha1$nsample==250], mse.alpha1$mse.naive[mse.alpha1$nsample==250], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 ) lines(mse.alpha1$lambda[mse.alpha1$nsample==250],mse.alpha1$mse.RegCal[mse.alpha1$nsample==250],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample==250],mse.alpha1$mse.PL[mse.alpha1$nsample==250],col=3,lty=3) title ( expression (paste (Mean squared error for , alpha[1])), cex.main=1.5) title(\n\n sample size=250) legend(.7,1, legend= c(Naive, Regression Calibration, Pseudo Likelihood), bty = n,col=c(4,2,3),lty=c(4,2,3)) plot(mse.alpha1$lambda[mse.alpha1$nsample==1000], mse.alpha1$mse.naive[mse.alpha1$nsample== 1000], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 ) lines(mse.alpha1$lambda[mse.alpha1$nsample== 1000],mse.alpha1$mse.RegCal[mse.alpha1$nsample== 1000],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample== 1000],mse.alpha1$mse.PL[mse.alpha1$nsample== 1000],col=3,lty=3) title ( expression (paste (Mean squared error for , alpha[1])), cex.main=1.5) title(\n\n sample size=1000) legend(.7,1, legend= c(Naive, Regression Calibration, Pseudo Likelihood), bty = n,col=c(4,2,3),lty=c(4,2,3)) plot(mse.alpha2$lambda[mse.alpha2$nsample==50],
Re: [R] multiple graphs with a single legend and trellis graph
Dear Jim, first of all, thank you very much :) can you please explain me how to use split.screen? I’m felling so silly, I could not run your example because of x11(width=10,height=4). I already installed package XQuartz because X11 library was missing , nonetheless, after I have installed it, “ Error in .External2(C_X11, d$display, d$width, d$height, d$pointsize, : unable to start device X11 In addition: Warning message: In x11(width = 10, height = 4) : unable to open connection to X11 display ‘' I didn’t started the x11 server on my mac ;) Now I got the graphs ;) I attach my previous graphs and my data, so you can see :) I’m very naive and new in R :( Thanks again for your help ;) Atenciosamente, Rosa Oliveira Atenciosamente, Rosa Oliveira -- Rosa Celeste dos Santos Oliveira, E-mail: rosit...@gmail.com Tlm: +351 939355143 Linkedin: https://pt.linkedin.com/in/rosacsoliveira Many admire, few know Hippocrates On 08 Jul 2015, at 11:20, Jim Lemon drjimle...@gmail.com wrote: Hi Rosa, As you are using base graphics, here is an example that might be of use. As we don't have access to your data, I have used something similar to the toy data in the example for the panes function. This could be done better using the split.screen function, so let me know if you would like an example using that. library(plotrix) # start a wide plotting device x11(width=10,height=4) y-runif(100) oldpar-panes(matrix(1:6,nrow=2,byrow=TRUE),widths=c(1,1,1.7)) par(mar=c(0,2,1.8,0)) boxplot(y,axes=FALSE) axis(2) box() par(mar=c(0,0,1.8,0)) tab.title(Boxplot of y,tab.col=#88dd88,cex=1) y_hist-hist(y,axes=FALSE,breaks=seq(0,1,length.out=5)) box() tab.title(Histogram of y,tab.col=#dd8800,cex=1) par(mar=c(0,0,1.8,12)) pie(y_hist$counts,col=2:9) tab.title(Pie chart of y categories,tab.col=#dd,cex=1) box() par(mar=c(2,2,1.8,0)) plot(y,xaxs=i,xlim=c(0,101),axes=FALSE,col=2:9) axis(2) box() tab.title(Scatterplot of y,tab.col=#aabbcc,cex=1) par(mar=c(2,0,1.8,0)) plot(sort(y),xaxs=i,xlim=c(0,101),axes=FALSE,col=2:9) box() tab.title(Scatterplot of y sorted,tab.col=#ddbc44,cex=1) # center the title at the middle of the fifth plot mtext(Overall title of plot,side=1,line=0.8,cex=1.5) par(mar=c(2,0,1.8,12)) plot(diff(y),xaxs=i,xlim=c(0,100),axes=FALSE,col=2:9) axis(4) box() tab.title(Scatterplot of diff(y),tab.col=#ff33cc,cex=1) legend(115,1.8, c(Boxplot,Histogram,Pie chart,Scatterplot,Sort,Diff), fill=c(#88dd88,#dd8800,#dd,#aabbcc,#ddbc44,#ff33cc), xpd=NA) Jim On Wed, Jul 8, 2015 at 1:05 PM, David Winsemius dwinsem...@comcast.net wrote: On Jul 7, 2015, at 2:45 PM, Rosa Oliveira wrote: Iam trying to plot 6 graphs in one single plot and I was able to, nonetheless I wanted that all graphs had just 1 common legend, as the legend is the same for all the 6 graphs and there is no sense in repeating it 6 times and even more, the legends in each graph sometimes don’t fit the graph. Is there a way to put just one legend for all the 6 graphs ate the same time? I was told to use a trellis graph, but after days of trying to do that I wasn’t able to. Can anyone help me? library(ggplot2) library(reshape) library(lattice) Why did you load those packages above? As far as I can see you did not use any lattice or ggplot2 functions. (Also see no reshape or reshape2 functions in use.) par(mfrow=c(2,3)) mse.alpha1 -read.csv(file=graphs_mse_alpha1.csv,head=TRUE,sep=,) And there you lose us. We are unable to see your data. The `legend` function can put the legend anywhere. You may need to set par(xpd=TRUE) if the location is outside the current plot area. If you wnated just one legend then you mus ask yourself why you are issuing multiple legend calls. I see the token-`legend` a total of 12 times in the code below. attach(mse.alpha1) names(mse1000.alpha1) mse.alpha2 -read.csv(file=graphs_mse_alpha2.csv,head=TRUE,sep=,) attach(mse.alpha2) names(mse.alpha2) nsample==50 plot(mse.alpha1$lambda[mse.alpha1$nsample==50], mse.alpha1$mse.naive[mse.alpha1$nsample==50], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 ) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.RegCal[mse.alpha1$nsample==50],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.PL[mse.alpha1$nsample==50],col=3,lty=3) title ( expression (paste (Mean squared error for , alpha[1])), cex.main=1.5) title(\n\n sample size=50) legend(.7,1, legend= c(Naive, Regression Calibration, Pseudo Likelihood), bty = n,col=c(4,2,3),lty=c(4,2,3)) plot(mse.alpha1$lambda[mse.alpha1$nsample==250], mse.alpha1$mse.naive[mse.alpha1$nsample==250],
Re: [R] R-project on App-V 5
http://cran.r-project.org/ and do not post further to this list, please. Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Wed, Jul 8, 2015 at 2:43 AM, Gilfred Tan gilfred@aberdeen-asset.com wrote: Hi Here at Aberdeen Asset Management . We are in the process of looking to move to a VDI environment (based on Win7) and are wanting to deploy the R-project via Microsoft App-V 5. Based around this I have a series of technical queries regarding your application. Firstly can I ask you to please provide me (or point me towards a download location) the current version of software, including an installation guide, and any updates / patches needed? The company that is packaging our applications into the App-V environment have asked us the following questions (feel free to point me to the install guide where applicable on these queries): - are there any pre-requisites (such as Java for instance) or dependant applications? - is the app 32-bit or 64-bit? - is there any 16-bit code in the app? - is it compatible with Win7 64 bit?. - does is support RDSH (64bit XenApp 7.6) - does it support App-V 5? - any other vendor technical support contact. - how are updates managed and what is their typical frequency? - Are there licensing details regarding the product, and if so please advise on how it is controlled / locked down. Please come back to me with any questions you may have on my requests, otherwise thanks in advance for the assistance. Regards Gilfred Tan Discovery Engineer Aberdeen Asset Management Asia Limited (Reg. No. 199105448E) Tel: +65 6395 2642 aberdeen-asset.comhttp://www.aberdeen-asset.com/ Find out how aspects of everyday life embody our philosophy at Aberdeen simplyaberdeen.comhttp://www.simplyaberdeen.com This email and any attachment are confidential and may contain privileged and copyright information. It is intended solely for the addressee. If you are not the intended recipient, please notify the sender immediately and delete this email. In accordance with good business practice and applicable regulations, all electronic communications with the Aberdeen Asset Management Group of companies may be monitored and retained. Aberdeen Asset Management PLC, Company Number: SC82015, Registered Office: Ten Queen's Terrace, Aberdeen AB10 1YG Scotland. For further information please visit our website: http://www.aberdeen-asset.com and www.aberdeen-asset.com/aam.nsf/AAM/privacy. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 graphs with a single legend and trellis graph
Dear Jim, first of all, thank you very much :) can you please explain me how to use split.screen? I attach my previous graphs and my data, so you can see :) I’m very naive and new in R :( I really tried: library(plotrix) # start a wide plotting device x11(width=10,height=4) y-runif(100) oldpar-panes(matrix(1:6,nrow=2,byrow=TRUE),widths=c(1,1,1.7)) par(mar=c(0,2,1.8,0)) mse - plot(mse.alpha1$lambda[mse.alpha1$nsample==50], mse.alpha1$mse.naive[mse.alpha1$nsample==50], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.RegCal[mse.alpha1$nsample==50],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample==50],mse.alpha1$mse.PL[mse.alpha1$nsample==50],col=3,lty=3) tab.title(alpha 1 N sample=50,tab.col=#88dd88,cex=1) # tab.title(\n\n sample size=50) # problem: when I run: tab.title(Mean squared error for , paste(alpha[1])),tab.col=#88dd88,cex=1) # I get an error message: unexpected string constant in tab.title(Mean squared error for , paste(alpha[1])),tab.col= # I searched but wasn't able to fix this one, neither the other subtitle: # tab.title(\n\n sample size=50) box() par(mar=c(0,0,1.8,0)) plot(mse.alpha1$lambda[mse.alpha1$nsample==250], mse.alpha1$mse.naive[mse.alpha1$nsample==250], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha1$lambda[mse.alpha1$nsample==250],mse.alpha1$mse.RegCal[mse.alpha1$nsample==250],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample==250],mse.alpha1$mse.PL[mse.alpha1$nsample==250],col=3,lty=3) tab.title ( alpha 1 N sample=250,tab.col=#dd8800,cex=1) box() plot(mse.alpha1$lambda[mse.alpha1$nsample==1000], mse.alpha1$mse.naive[mse.alpha1$nsample== 1000], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,1), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha1$lambda[mse.alpha1$nsample== 1000],mse.alpha1$mse.RegCal[mse.alpha1$nsample== 1000],col=2,lty=2) lines(mse.alpha1$lambda[mse.alpha1$nsample== 1000],mse.alpha1$mse.PL[mse.alpha1$nsample== 1000],col=3,lty=3) tab.title(alpha 1 N sample=1000,tab.col=#dd,cex=1) box() par(mar=c(2,2,1.8,0)) plot(mse.alpha2$lambda[mse.alpha2$nsample==50], mse.alpha2$mse.naive[mse.alpha2$nsample==50], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,.17), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha2$lambda[mse.alpha2$nsample==50],mse.alpha2$mse.RegCal[mse.alpha2$nsample==50],col=2,lty=2) lines(mse.alpha2$lambda[mse.alpha2$nsample==50],mse.alpha2$mse.PL[mse.alpha2$nsample==50],col=3,lty=3) box() tab.title(alpha 2 N sample=50,tab.col=#aabbcc,cex=1) par(mar=c(2,0,1.8,0)) plot(mse.alpha2$lambda[mse.alpha2$nsample==250], mse.alpha2$mse.naive[mse.alpha2$nsample==250], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,.17), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha2$lambda[mse.alpha2$nsample==250],mse.alpha2$mse.RegCal[mse.alpha2$nsample==250],col=2,lty=2) lines(mse.alpha2$lambda[mse.alpha2$nsample==250],mse.alpha2$mse.PL[mse.alpha2$nsample==250],col=3,lty=3) box() tab.title(alpha 2 N sample=250,tab.col=#ddbc44,cex=1) # center the title at the middle of the fifth plot mtext(Mean Squared Error,side=1,line=0.8,cex=1.5) par(mar=c(2,0,1.8,12)) plot(mse.alpha2$lambda[mse.alpha2$nsample==1000], mse.alpha2$mse.naive[mse.alpha2$nsample== 1000], xlab=expression(paste(lambda)),ylab=MSE,type=l,col=4,lty=4, xlim=c(.6,1), ylim=c(0,.17), cex.lab=1.5 #,main=yaxs default ) lines(mse.alpha2$lambda[mse.alpha2$nsample== 1000],mse.alpha2$mse.RegCal[mse.alpha2$nsample==250],col=2,lty=2) lines(mse.alpha2$lambda[mse.alpha2$nsample== 1000],mse.alpha2$mse.PL[mse.alpha2$nsample== 1000],col=3,lty=3) box() tab.title(alpha 2 N sample=1000,tab.col=#ff33cc,cex=1) legend(115,1.8, c(alpha 1 N sample=50,alpha 1 N sample=250,alpha 1 N sample=1000, alpha 2 N sample=50,alpha 2 N sample=250,alpha 2 N sample=1000), fill=c(#88dd88,#dd8800,#dd,#aabbcc,#ddbc44,#ff33cc), xpd=NA) legend(115,1.8, c(Naive, Regression Calibration, Pseudo Likelihood), bty = n,col=c(4,2,3),lty=c(4,2,3), xpd=NA) and I got: Thanks again for your help ;) Atenciosamente, Rosa Oliveira -- Rosa Celeste dos Santos Oliveira, E-mail: rosit...@gmail.com Tlm: +351 939355143 Linkedin: https://pt.linkedin.com/in/rosacsoliveira Many admire, few know Hippocrates On 08 Jul 2015, at 11:35, Dennis Murphy djmu...@gmail.com wrote: Hi: The general process for doing this kind of thing in either ggplot2 or lattice
Re: [R] Hypergeometric Function seems to give wrong results
Carlos Nasher via R-help r-help at r-project.org writes: [snip] I need to evaluate the Hypergeometric Function of the 2nd kind (Tricomi confluent hypergeometric function). Therefore I'm using the kummerU function from the fAsianOptions package. It seems to me that kummerU is giving wrong results. Here's an example: library(fAsianOptions) kummerU(a=19, b=19, x = 10) R gives 1838.298 for the real part. If I use Mathematica via the wolfram site ( http://functions.wolfram.com/webMathematica /FunctionEvaluation.jsp?name=HypergeometricU) the result is 3.52603e-20 which is more reasonable in the context of my analysis. [snip] Your best bet is probably to contact the package maintainer (use maintainer(fAsianOptions) to see who it is, or look on the CRAN page for the package). If this functionality is very commonly used in finance you might try the r-sig-finance mailing list (indicating that you've already tried here). good luck Ben Bolker __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 graphs with a single legend and trellis graph
Dear Jim, first of all, thank you very much :) when I run the code: myDF - rbind(mse.alpha1, mse.alpha2) # assumes both data frames have the same variables in the same order myDF$ID - factor(rep(c(alpha1, alpha2), times = c(nrow(mse.alpha1), nrow(mse.alpha2))) ) library(reshape2) myDF.melt - melt(myDF, id = c(ID, nsample, lambda), measure = c(mse.naive, mse.RegCal, mse.PL)) #Melt the three columns to be plotted, something like library(ggplot2) ggplot(myDF.melt, aes(x = lambda, y = value, color = variable)) + geom_point() + geom_line() + facet_grid(ID ~ nsample) + labs(x = expression(paste(lambda)), y = MSE, color = Type”) I get the attached graph. I also attach my data, so you can see :) I’m I able to resize the graphs differently? I.e. for alpha1: ylim=ylim=c(0,.6) and for alpha2: ylim=c(0,.17)? I reshaped, a new variable in sample was created, NA, Was it me that made something wrong? I’m very naive and new in R :( Thanks again ;) Atenciosamente, Rosa Oliveira -- Rosa Celeste dos Santos Oliveira, E-mail: rosit...@gmail.com Tlm: +351 939355143 Linkedin: https://pt.linkedin.com/in/rosacsoliveira Many admire, few know Hippocrates __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] add a special column to a matrix
Hi Lida, I think what you want is: mat1-read.table(text=abc d fg1:23 dfgv 5 pt10:18 tgtgh 1 wq 15:123oiljk 6 fg 9:1323ass 4 yr 12:123kjjlk 5,header=TRUE) mat2-read.table(text=b q 1:23 0 10:18 1 14:4552 15:1232 9:13232 12:1231 5:15480,header=TRUE) merge(mat1,mat2,by=b) You don't seem to have a column name for the first column in mat2, so I have added one. If it is different from mat1, you will have to use a slightly different b argument. Jim On Wed, Jul 8, 2015 at 4:06 PM, PIKAL Petr petr.pi...@precheza.cz wrote: Hi See answers in line From: Lida Zeighami [mailto:lid.z...@gmail.com] Sent: Tuesday, July 07, 2015 10:20 PM To: PIKAL Petr Subject: Re: [R] add a special column to a matrix Hi Petr, Thanks, I can solve it! On Jul 7, 2015 11:05 AM, Lida Zeighami lid.z...@gmail.commailto:lid.z...@gmail.com wrote: Hi Petr, Thank you so much for replying! I have two problems: 1. I couldn't understand what you mean No HTML posting , would you please explain more about that? PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. 2. still my problem hasn't been solved! I don't want to add the columns and rows of two matrices together! just I want to add the q column from mat2 to mat1 ( column b in mat1 and the rownames in mat1 are the same but not in a same order! ) I should keep the mat1 and just add the value of rownames of mat2 to the equivalent elements in column b( I should add column q from mat2 to mat1 regarding the column b) Did you try read help page of merge command? Did you even try merge? If yes please describe what you do not like about it. merge(mat1, mat2, all.x=TRUE) shall take all lines of mat1 and add corresponding columns of mat2 to appropriate rows. However we do not know anything about your data. From your posting it seems to me that dim(mat1) results in c(n,4) and dim(mat2) results in (n,1) and what do you consider as a column in mat2 are row names. In that case you need to add a column of row names, maybe mat2$b - rownames(mat2) before calling merge Cheers Petr head(mat1) a b c d fg1:23 dfgv 5 pt10:18 tgtgh 1 wq 15:123oiljk 6 fg 9:1323ass 4 yr 12:123kjjlk 5 my second matrix: head(mat2) q 1:23 0 10:18 1 14:455 2 15:123 2 9:13232 12:1231 5:15480 output should be : head(mat) a b c d q fg1:23 dfgv 50 pt10:18 tgtgh 11 wq 15:123oiljk 62 fg 9:1323ass 42 yr 12:123kjjlk 51 Thanks again, Lida On Tue, Jul 7, 2015 at 9:53 AM, PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz wrote: Hi No HTML posting please, sometimes the mail is unreadable It is a work for merge. mat3 - merge(mat1, mat2, all=TRUE) shall do the trick (untested) Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org] On Behalf Of Lida Zeighami Sent: Tuesday, July 07, 2015 4:43 PM To: r-help@r-project.orgmailto:r-help@r-project.org Subject: [R] add a special column to a matrix Hi there, I have a two matrices which they have a common column! I want to add the a column of second to matrix to the equivalent column of first matrix! my first matrix is head(mat1) a b c d fg1:23 dfgv 5 pt10:18 tgtgh 1 wq 15:123oiljk 6 fg 9:1323ass 4 yr 12:123kjjlk 5 my second matrix: head(mat2) eq 1:23 0 10:18 1 14:455 2 15:123 2 9:13232 12:1231 5:15480 mat1 and mat2 have a common column (b and e) but is not in the same order, I want to add the q column from mat2 to be added to mat1 my output will be: head(mat) a b c d q fg1:23 dfgv 50 pt10:18 tgtgh 11 wq 15:123oiljk 62 fg 9:1323ass 42 yr 12:123kjjlk 51 would you please let me know how to do it? Thanks [[alternative HTML version deleted]] __ R-help@r-project.orgmailto:R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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-project on App-V 5
Please do read the posting guide ( http://www.R-project.org/posting-guide.html http://www.r-project.org/posting-guide.html). It points to the FAQ which answers much of your questions (http://cran.r-project.org/faqs.html). ir. Thierry Onkelinx Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest team Biometrie Kwaliteitszorg / team Biometrics Quality Assurance Kliniekstraat 25 1070 Anderlecht Belgium To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher The plural of anecdote is not data. ~ Roger Brinner The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey 2015-07-08 11:43 GMT+02:00 Gilfred Tan gilfred@aberdeen-asset.com: Hi Here at Aberdeen Asset Management . We are in the process of looking to move to a VDI environment (based on Win7) and are wanting to deploy the R-project via Microsoft App-V 5. Based around this I have a series of technical queries regarding your application. Firstly can I ask you to please provide me (or point me towards a download location) the current version of software, including an installation guide, and any updates / patches needed? The company that is packaging our applications into the App-V environment have asked us the following questions (feel free to point me to the install guide where applicable on these queries): - are there any pre-requisites (such as Java for instance) or dependant applications? - is the app 32-bit or 64-bit? - is there any 16-bit code in the app? - is it compatible with Win7 64 bit?. - does is support RDSH (64bit XenApp 7.6) - does it support App-V 5? - any other vendor technical support contact. - how are updates managed and what is their typical frequency? - Are there licensing details regarding the product, and if so please advise on how it is controlled / locked down. Please come back to me with any questions you may have on my requests, otherwise thanks in advance for the assistance. Regards Gilfred Tan Discovery Engineer Aberdeen Asset Management Asia Limited (Reg. No. 199105448E) Tel: +65 6395 2642 aberdeen-asset.comhttp://www.aberdeen-asset.com/ Find out how aspects of everyday life embody our philosophy at Aberdeen simplyaberdeen.comhttp://www.simplyaberdeen.com This email and any attachment are confidential and may contain privileged and copyright information. It is intended solely for the addressee. If you are not the intended recipient, please notify the sender immediately and delete this email. In accordance with good business practice and applicable regulations, all electronic communications with the Aberdeen Asset Management Group of companies may be monitored and retained. Aberdeen Asset Management PLC, Company Number: SC82015, Registered Office: Ten Queen's Terrace, Aberdeen AB10 1YG Scotland. For further information please visit our website: http://www.aberdeen-asset.com and www.aberdeen-asset.com/aam.nsf/AAM/privacy. [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] lattice::subscripts[?] usage question
Dear useRs,
I have a question regarding panel functions in the lattice package, in
particular how to customize the plotting colors in xyplot.
I have longitudinal data from several treatments (TRT) with subjects (SUBJ)
nested in treatment. Each subject has several time points; the time points are
nearly balanced across subjects, although not completely. At each sample
(SAMP) at each time point (TIME), two replicates (REP) are taken. Let's call
the response Y and the whole data.frame DAT.
My goal is to make a trellis plot with each treatment in its own panel, each
subject having its own color and lines connecting the REPs within SAMP (after
adding jitter along the TIME axis to distinguish SUBJs). Let me switch over to
an explicit example with artificial data.
set.seed(695442223)
DAT - data.frame(TRT=factor(rep(c(Trt1,Trt2), each=12)), #
2 treatments
SUBJ=factor(paste('subj', rep(seq(4), each=6), sep='')), #
4 subjects, 2 w/in each TRT
SAMP=factor(rep(seq(12), each=2)), #
4x3 = 12 samples
REP=factor(c(1,2)), #
2 replicates
TIME=rep(c(4,4,8,8,12,12), times=4), #
3 arbitrary times
Y=round(rep(rgamma(n=12, shape=47500, scale=1/500),
each=2) +
rep(rgamma(n=12, shape=4, scale=1/8), each=2) *
c(-1,1),
2) # arbitrary Y but very easy to view
)
DAT - transform(DAT,
# horizontal jitter
plotX=TIME+ifelse(SUBJ %in% c(subj1,subj3), -1,1)/10,
# unique plotting color for each subject
COLS=factor(c( green, black, blue,
red))[as.numeric(SUBJ)]
)
The canonical example is:
xyplot(Y ~ plotX | TRT, data = DAT, groups = SAMP, type=b)
Of course, this connects the REPs within SAMP, since SAMP is the groups
variable. But each SAMP is now independently colored, recycled from (if I
understand correctly) trellis.par.get('superpose.symbol/line')$col, instead
of each SUBJ being independently colored from the COLS variable.
In Section 5.2 in Deepayan Sarkar's Lattice: Multivariate Data Visualization
with R (Springer 2008), the suggestion in Section 5.2 is to use a panel
function which gets passed an explicit subscripts argument, to distinguish
the groups indexing from the color indexing. Starting with the book's code to
plot Figure 5.4, I hacked around to get this:
xyplot(Y ~ plotX | TRT, data = DAT, groups = SAMP, type=b,
# the full vector of colors
cols = DAT[['COLS']],
panel = function(x, y, ..., cols, groups, subscripts) {
colSUBJ - cols[subscripts]
panel.xyplot(x, y, groups=groups,
subscripts=subscripts,
..., col.line=colSUBJ,
col.symbol=colSUBJ)
}
)
Now this gets each treatment TRT with its own color, but not each subject SUBJ.
I am indeed not exactly sure what this code does specifically, with the
subscripts argument. But nearly every other permutation of arguments I could
think off either gave a totally wrong plot, or an error.
How do I write a panel function to join reps in the same sample with the groups
argument, but give each subject a unique color? (an alternate chore is to use
only unique colors within each treatment, or repeating colors in different
treatments). And what is a good pointer or two to good resources explaining
the use of the subscripts argument in panel functions? Sarkar's book is
fantastic but its treatment of this issue is quite thin.
Thanks,
John Szumiloski
John Szumiloski, Ph.D.
Principal Scientist, Statistician
Analytical and Bioanalytical Development
NBR105-1-1411
Bristol-Myers Squibb
P.O. Box 191
1 Squibb Drive
New Brunswick, NJ
08903-0191
(732) 227-7167
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Re: [R-es] Crear un GUI para R con tcltk
No opinaré sobre el código puesto que no lo leí. Pero comentar que en
particular he tenido problemas copiando datos desde excel, en general me
resulta mejor copiarlos de excel, pegarlos en un editor de texto
cualquiera y luego copiarlos a R. Por que? Ni idea, como lo he usado
puntualmente no me he puesto a profundizar en el tema, pero he tenido
ese problema.
Saludos
DMTV Fernando Macedo
Ayudante del área Mejoramiento Genético
Facultad de Veterinaria - UdelarR - Uruguay
Tel: 26284291
Cel.: 098596947
ferm...@gmail.com
El 08/07/15 a las 09:54, Jesús Para Fernández escribió:
BUenas,
Quiero crear un GUI muy simple, el cual consiste en una ventana, que al
abrirse tiene dos botones. El primer boton, copiar, es un boton que ejecutar�a
datos-read.table(clipboard,header=T,dec=,,sep=\t)
Y el segundo boton muestra todos los data.frames que hay en R
Para ello, estoy usando tcltk, por lo que hago lo siguiente:
require(tcltk)
tt - tktoplevel()
tktitle(tt) - Mi primer programa
# Create a variable to keep track of the state of the dialog window:
# If the window is active,done = 0
# If the window has been closed using the OK button, done =
1
# If the window has been closed using the Cancel button or destroyed, done =
2
done - tclVar(0) # tclVar() creates a Tcl variable
# Create two buttons and for each one, set the value of the done variable
# to an appropriate value
OK.but - tkbutton(tt, text = OK ,
command = function() tclvalue(done) - 1)
Cancel.but - tkbutton(tt, text = Cancel,
command = function() tclvalue(done) - 2)
# Place the two buttons on the same row in their assigned window (tt)
tkgrid(OK.but, Cancel.but)
# Capture the event Destroy (e.g. Alt-F4 in Windows) and when this happens,
# assign 2 to done
tkbind(tt, Destroy, function() tclvalue(done) - 2)
tkfocus(tt) # Place the focus to our tk window
# Do not proceed with the following code until the variable done is non-zero.
# (but other processes can still run, i.e., the system is not frozen)
tkwait.variable(done)
# The variable done is now non-zero, so we would like to record its value
before
# destroying the window tt. If we destroy it first, then done will be set to
2
# because of our earlier binding, but we want to determine whether the user
# pressed OK (i.e., see whether done is equal to 1)
doneVal - as.integer(tclvalue(done)) # Get and coerce content of a Tcl
variable
tkdestroy(tt)
# Test the result
if (doneVal == 1) {
datos-read.table(clipboard,header=T,dec=,,sep=\t)
}
if (doneVal == 2) {
ls()
}
Esto funciona al crearlo en el script de R, pero el poortapapeles no me copia
las celdas de excel, sino todo el c�digo anterior.
Podeis echarme una mano??
Gracias!!!
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[R] select a subset of a matrix which one of its column meet a condition
Hi there, I have a matrix and I want to get a subset from that which one of its matrix meet a condition, my matrix is met Row.names Name maf caf 1 10:13915 10:139 0.0003782148 0.0003782148 2 10:18738 10:18738 0.0003759398 0.0003759398 3 10:100011321 10:100011321 0.0003762227 0.0003762227 4 10:100012219 10:100012219 0.0007518797 0.0007518797 5 10:100013325 10:100013325 0.00 0.00 6 10:100015404 10:100015404 0.00 0.00 I want to choose a subset from met which maf values are between 0 and 0.05 (0,0.05) I wrote this code, but seem doesn't work properly: maf- met[which(c(met[,5]) %in% c(0,0.05)),] the dim(maf) is 0 so seems my code didn't work! would please let me know how to correct it? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] select a subset of a matrix which one of its column meet a condition
Hello, Your matrix has only 4 columns but you refer to met[,5]. I'll assume you're refering to the last column, met[,4]. Try reading the help page for ?%in%, it doesn't do what you seem to think it does. And try using =. maf - met[0 = met[, 4] met[, 4] = 0.05, ] Hope this helps, Rui Barradas Em 08-07-2015 16:37, Lida Zeighami escreveu: Hi there, I have a matrix and I want to get a subset from that which one of its matrix meet a condition, my matrix is met Row.names Name maf caf 1 10:13915 10:139 0.0003782148 0.0003782148 2 10:18738 10:18738 0.0003759398 0.0003759398 3 10:100011321 10:100011321 0.0003762227 0.0003762227 4 10:100012219 10:100012219 0.0007518797 0.0007518797 5 10:100013325 10:100013325 0.00 0.00 6 10:100015404 10:100015404 0.00 0.00 I want to choose a subset from met which maf values are between 0 and 0.05 (0,0.05) I wrote this code, but seem doesn't work properly: maf- met[which(c(met[,5]) %in% c(0,0.05)),] the dim(maf) is 0 so seems my code didn't work! would please let me know how to correct it? Thanks [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to assign value to a variable dynamically constructed
You can use an environment instead of a list using the same [[ syntax. It is like 'get0(..., inherit=FALSE)' on the left side of the - and like 'assign(...)' on the right side. E.g., myData - new.env() varName - v1 myData[[varName]] - 1:10 myData[[varName]][4] - myData[[varName]][4] * 100 myData[[varName]] # [1] 1 2 3 400 5 6 7 8 9 10 names(myData) # [1] v1 (Before R-3.2.0 or so, you had to use objects(myData,all=TRUE) if myData was an environment and names(myData) if it was a list. Now names() works for environments.) It is better to use a dedicated environment (or list) for each set of related variables so that name collisions do not cause problems. Bill Dunlap TIBCO Software wdunlap tibco.com On Wed, Jul 8, 2015 at 10:06 AM, Greg Snow 538...@gmail.com wrote: This is FAQ 7.21. The most important part of the answer in FAQ 7.21 is the last section where it states that it is often easier to use a list rather than messing around with trying to dynamically name global variables. If you tell us what you are trying to accomplish then we may have better advice. The route you are headed down now usually leads to inefficient code and hard to find bugs. On Tue, Jul 7, 2015 at 2:53 PM, Jun Shen jun.shen...@gmail.com wrote: Dear list, Let's say we have a variable (id), whose name is dynamically constructed. This variable represents a vector or data frame with many elements. Now I want to specifically assign a value to one of the elements. I couldn't get it right. test - 'id' # id is dynamically constructed through paste() id - 1:4 # I can get the element by doing get(test)[2] # Now I want to assign a value to the second element of this dynamical variable. get(test)[2] - 5 # doesn't work. Thanks a lot. Jun Shen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to assign value to a variable dynamically constructed
This is FAQ 7.21. The most important part of the answer in FAQ 7.21 is the last section where it states that it is often easier to use a list rather than messing around with trying to dynamically name global variables. If you tell us what you are trying to accomplish then we may have better advice. The route you are headed down now usually leads to inefficient code and hard to find bugs. On Tue, Jul 7, 2015 at 2:53 PM, Jun Shen jun.shen...@gmail.com wrote: Dear list, Let's say we have a variable (id), whose name is dynamically constructed. This variable represents a vector or data frame with many elements. Now I want to specifically assign a value to one of the elements. I couldn't get it right. test - 'id' # id is dynamically constructed through paste() id - 1:4 # I can get the element by doing get(test)[2] # Now I want to assign a value to the second element of this dynamical variable. get(test)[2] - 5 # doesn't work. Thanks a lot. Jun Shen [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Gregory (Greg) L. Snow Ph.D. 538...@gmail.com __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] Maxent Jarfile
Hi,
I have been trying to solve the below problem for 2 days with no success.
Hopefully you can help as i can find no assistance online.
I am attempting to run the niche.equivalency.test and the bg.similarity.test
using RStudio and Maxent. I keep getting the error:
Error: Unable to access jarfile C:/ProgramError in file(fname, r) : cannot
open the connectionIn addition: Warning messages:1: running command 'java -jar
C:/Program Files/R/R-3.1.3/library/dismo/java/maxent.jar -e
R.phyloclim.temp/background.csv -s R.phyloclim.temp/samples.csv -j
R.phyloclim.temp/proj/ -o R.phyloclim.temp/out/ -r removeduplicates
nopictures autorun' had status 1 2: In file(fname, r) : cannot open file
'R.phyloclim.temp/out/Rhinolophus blasii_proj.asc': No such file or directory
I suspect the issue is that the file directory doesnt have , but i have no
idea how to add these in, as in RStudio values, the does appear.
My code is:
# load required
packageslibrary(raster)library(mgcv)library(dismo)library(rgdal)library(ellipse)library(sp)library(proj4)library(rgeos)
library(rJava)library(maptools)library(rasterVis)library(phyloclim)
# path to MAXENT# --maxent.exe -
paste(system.file(package=dismo), /java/maxent.jar, sep
= )
# a data frame of coordinates where two species # have been detected ('presence
points') and# a raster stack of environmental covariables#
--
###Change to correct species usedfile - paste(system.file(package=dismo),
/ex/Rhinolophus_species.csv, sep=)# this is the file we will use:file
#save(file, file=Molossidae_rarefied_points.rda)
#data()#data(package = .packages(all.available = TRUE))
#myData - read.csv(file, header=TRUE, nrows=1)
Rhinolophus_species - read.table(file, header=TRUE, sep=',')
species - c(Rhinolophus blasii, Rhinolophus clivosus)#data(sites)samples
- Rhinolophus_species[grep(paste(species, collapse = |),
Rhinolophus_species$Spp), ]data.path - system.file(extdata, package =
phyloclim)preds - list.files(path = data.path, pattern = [.]asc)preds -
paste(data.path, preds, sep = /)preds - stack(lapply(X = preds, FUN =
raster))
# testing against 9 permutations of the data#
---reps - 1000
# run hypothesis tests# if (file.exists(maxent.exe)){ net
- niche.equivalency.test(samples, preds, reps, maxent.exe) net; plot(net)
bst - bg.similarity.test(samples, preds, reps, app = maxent.exe) bst;
plot(bst)} else { message(get a copy of MAXENT (see Details))}
[[alternative HTML version deleted]]
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[R] norm's book
Hi All: In case anyone is interested, Norm's new book, parallel computing for data science is out on amazon. It already got raving reviews from Dave Giles who runs a popular econometrics blog. Mark [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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-es] Lectura de ficheros externos
Tengo un fichero Excel con datos numericos con comas (Ej:6,4523). Tengo que trabajar con dichos datos en R. Como puedo hacerlo? [[alternative HTML version deleted]] ___ R-help-es mailing list R-help-es@r-project.org https://stat.ethz.ch/mailman/listinfo/r-help-es
Re: [R] Maxent Jarfile
Hi Annemarie,
You have sent the email in HTML and it is very close to unreadable. Could you
please resubmit the message in plain text. R-help does not accept HTML and, as
happened here, the text gets seriously mangled.
John Kane
Kingston ON Canada
-Original Message-
From: annemarie...@hotmail.com
Sent: Wed, 8 Jul 2015 20:22:57 +
To: r-help@r-project.org
Subject: [R] Maxent Jarfile
Hi,
I have been trying to solve the below problem for 2 days with no success.
Hopefully you can help as i can find no assistance online.
I am attempting to run the niche.equivalency.test and the
bg.similarity.test using RStudio and Maxent. I keep getting the error:
Error: Unable to access jarfile C:/ProgramError in file(fname, r) :
cannot open the connectionIn addition: Warning messages:1: running
command 'java -jar C:/Program
Files/R/R-3.1.3/library/dismo/java/maxent.jar -e
R.phyloclim.temp/background.csv -s R.phyloclim.temp/samples.csv -j
R.phyloclim.temp/proj/ -o R.phyloclim.temp/out/ -r removeduplicates
nopictures autorun' had status 1 2: In file(fname, r) : cannot open
file 'R.phyloclim.temp/out/Rhinolophus blasii_proj.asc': No such file or
directory
I suspect the issue is that the file directory doesnt have , but i have
no idea how to add these in, as in RStudio values, the does appear.
My code is:
# load required
packageslibrary(raster)library(mgcv)library(dismo)library(rgdal)library(ellipse)library(sp)library(proj4)library(rgeos)
library(rJava)library(maptools)library(rasterVis)library(phyloclim)
# path to MAXENT# --maxent.exe -
paste(system.file(package=dismo),
/java/maxent.jar, sep = )
# a data frame of coordinates where two species # have been detected
('presence points') and# a raster stack of environmental covariables#
--
###Change to correct species usedfile -
paste(system.file(package=dismo), /ex/Rhinolophus_species.csv,
sep=)# this is the file we will use:file
#save(file, file=Molossidae_rarefied_points.rda)
#data()#data(package = .packages(all.available = TRUE))
#myData - read.csv(file, header=TRUE, nrows=1)
Rhinolophus_species - read.table(file, header=TRUE, sep=',')
species - c(Rhinolophus blasii, Rhinolophus
clivosus)#data(sites)samples - Rhinolophus_species[grep(paste(species,
collapse = |), Rhinolophus_species$Spp), ]data.path -
system.file(extdata, package = phyloclim)preds - list.files(path =
data.path, pattern = [.]asc)preds - paste(data.path, preds, sep =
/)preds - stack(lapply(X = preds, FUN = raster))
# testing against 9 permutations of the data#
---reps - 1000
# run hypothesis tests# if (file.exists(maxent.exe)){
net - niche.equivalency.test(samples, preds, reps, maxent.exe) net;
plot(net) bst - bg.similarity.test(samples, preds, reps, app =
maxent.exe) bst; plot(bst)} else { message(get a copy of MAXENT (see
Details))}
[[alternative HTML version deleted]]
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PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!
__
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and provide commented, minimal, self-contained, reproducible code.
Re: [R] multiple graphs with a single legend and trellis graph
Hi Rosa, Neither the graph nor the data arrived. R-help can be very fussy about what attached files it will accept. Usually pdf, txt and png, I think, will come through. In any case it is much better to supply data using the dput() function See ?dput or have a look at http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example and http://adv-r.had.co.nz/Reproducibility.html for how to do this. It is best to use dput() rather than supplying a data file because dput() ensures that we get an exact copy of the data as it exists on your computer. There is no real guarantee that I will read in a data file the same way as you have. John Kane Kingston ON Canada -Original Message- From: rosit...@gmail.com Sent: Wed, 8 Jul 2015 13:11:34 +0100 To: djmu...@gmail.com, drjimle...@gmail.com, r-help@r-project.org Subject: Re: [R] multiple graphs with a single legend and trellis graph Dear Jim, first of all, thank you very much :) when I run the code: myDF - rbind(mse.alpha1, mse.alpha2) # assumes both data frames have the same variables in the same order myDF$ID - factor(rep(c(alpha1, alpha2), times = c(nrow(mse.alpha1), nrow(mse.alpha2))) ) library(reshape2) myDF.melt - melt(myDF, id = c(ID, nsample, lambda), measure = c(mse.naive, mse.RegCal, mse.PL)) #Melt the three columns to be plotted, something like library(ggplot2) ggplot(myDF.melt, aes(x = lambda, y = value, color = variable)) + geom_point() + geom_line() + facet_grid(ID ~ nsample) + labs(x = expression(paste(lambda)), y = MSE, color = Type”) I get the attached graph. I also attach my data, so you can see :) I’m I able to resize the graphs differently? I.e. for alpha1: ylim=ylim=c(0,.6) and for alpha2: ylim=c(0,.17)? I reshaped, a new variable in sample was created, NA, Was it me that made something wrong? I’m very naive and new in R :( Thanks again ;) Atenciosamente, Rosa Oliveira -- Rosa Celeste dos Santos Oliveira, E-mail: rosit...@gmail.com Tlm: +351 939355143 Linkedin: https://pt.linkedin.com/in/rosacsoliveira Many admire, few know Hippocrates __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] add a special column to a matrix
Hi See answers in line From: Lida Zeighami [mailto:lid.z...@gmail.com] Sent: Tuesday, July 07, 2015 10:20 PM To: PIKAL Petr Subject: Re: [R] add a special column to a matrix Hi Petr, Thanks, I can solve it! On Jul 7, 2015 11:05 AM, Lida Zeighami lid.z...@gmail.commailto:lid.z...@gmail.com wrote: Hi Petr, Thank you so much for replying! I have two problems: 1. I couldn't understand what you mean No HTML posting , would you please explain more about that? PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. 2. still my problem hasn't been solved! I don't want to add the columns and rows of two matrices together! just I want to add the q column from mat2 to mat1 ( column b in mat1 and the rownames in mat1 are the same but not in a same order! ) I should keep the mat1 and just add the value of rownames of mat2 to the equivalent elements in column b( I should add column q from mat2 to mat1 regarding the column b) Did you try read help page of merge command? Did you even try merge? If yes please describe what you do not like about it. merge(mat1, mat2, all.x=TRUE) shall take all lines of mat1 and add corresponding columns of mat2 to appropriate rows. However we do not know anything about your data. From your posting it seems to me that dim(mat1) results in c(n,4) and dim(mat2) results in (n,1) and what do you consider as a column in mat2 are row names. In that case you need to add a column of row names, maybe mat2$b - rownames(mat2) before calling merge Cheers Petr head(mat1) a b c d fg1:23 dfgv 5 pt10:18 tgtgh 1 wq 15:123oiljk 6 fg 9:1323ass 4 yr 12:123kjjlk 5 my second matrix: head(mat2) q 1:23 0 10:18 1 14:455 2 15:123 2 9:13232 12:1231 5:15480 output should be : head(mat) a b c d q fg1:23 dfgv 50 pt10:18 tgtgh 11 wq 15:123oiljk 62 fg 9:1323ass 42 yr 12:123kjjlk 51 Thanks again, Lida On Tue, Jul 7, 2015 at 9:53 AM, PIKAL Petr petr.pi...@precheza.czmailto:petr.pi...@precheza.cz wrote: Hi No HTML posting please, sometimes the mail is unreadable It is a work for merge. mat3 - merge(mat1, mat2, all=TRUE) shall do the trick (untested) Cheers Petr -Original Message- From: R-help [mailto:r-help-boun...@r-project.orgmailto:r-help-boun...@r-project.org] On Behalf Of Lida Zeighami Sent: Tuesday, July 07, 2015 4:43 PM To: r-help@r-project.orgmailto:r-help@r-project.org Subject: [R] add a special column to a matrix Hi there, I have a two matrices which they have a common column! I want to add the a column of second to matrix to the equivalent column of first matrix! my first matrix is head(mat1) a b c d fg1:23 dfgv 5 pt10:18 tgtgh 1 wq 15:123oiljk 6 fg 9:1323ass 4 yr 12:123kjjlk 5 my second matrix: head(mat2) eq 1:23 0 10:18 1 14:455 2 15:123 2 9:13232 12:1231 5:15480 mat1 and mat2 have a common column (b and e) but is not in the same order, I want to add the q column from mat2 to be added to mat1 my output will be: head(mat) a b c d q fg1:23 dfgv 50 pt10:18 tgtgh 11 wq 15:123oiljk 62 fg 9:1323ass 42 yr 12:123kjjlk 51 would you please let me know how to do it? Thanks [[alternative HTML version deleted]] __ R-help@r-project.orgmailto:R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting- guide.html and provide commented, minimal, self-contained, reproducible code. Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům. Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému. Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat. Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu. V případě, že je tento e-mail součástí obchodního jednání: - vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení
Re: [R] why must a named colClasses in read.table be in correct order
Thanks for insisting; I was wrong and I'm happy to see that there is
indeed code intended for named 'colClasses', which even goes back to
2004. But as you report, then names only work when
length(colClasses) cols (which also explains why I though it was not
supported). I'm not sure if that _strictly less than_ test is
intentional or a mistake, but I would propose the following patch:
[HB-X201]{hb}: svn diff src\library\utils\R\readtable.R
Index: src/library/utils/R/readtable.R
===
--- src/library/utils/R/readtable.R (revision 68642)
+++ src/library/utils/R/readtable.R (working copy)
@@ -139,7 +139,7 @@
if (rlabp) col.names - c(row.names, col.names)
nmColClasses - names(colClasses)
-if(length(colClasses) cols)
+if(length(colClasses) = cols)
if(is.null(nmColClasses)) {
colClasses - rep_len(colClasses, cols)
} else {
Your example works with this patch. I've made it source():able so you
can try it out (if you cannot source() https://, then download the
file an source it locally):
source(https://gist.githubusercontent.com/HenrikBengtsson/ed1eeb41a1b4d6c43b47/raw/ebe58f76e518dd014423bea466a5c93d2efd3c99/readtable-fix.R;)
kkk - c(a\tb,
3.14\tx)
colClasses - c(a=numeric, b=character)
data - read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = colClasses)
str(data)
### 'data.frame': 1 obs. of 2 variables:
### $ a: num 3.14
### $ b: chr x
## Does not work with utils::read.table(), but with patch
data - read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = rev(colClasses))
str(data)
### 'data.frame': 1 obs. of 2 variables:
### $ a: num 3.14
### $ b: chr x
Let's hope that the above is a (10-year old) typo, and changing a to
a = adds support for named 'colClasses', which is a really useful
functionality.
/Henrik
On Wed, Jul 8, 2015 at 6:42 PM, Andreas Leha
andreas.l...@med.uni-goettingen.de wrote:
Hi Henrik,
Thanks for your reply.
I am not (yet) convinced, though. The help page for read.table
mentions named colClasses and if I specify colClasses for not all
columns, the names are taken into account:
--8---cut here---start-8---
kkk - c(a\tb,
3.14\tx)
str(read.table(textConnection(kkk),
sep=\t,
header = TRUE))
str(read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses=c(b=character)))
--8---cut here---end---8---
What am I missing?
Best,
Andreas
On 09/07/2015 02:21, Henrik Bengtsson wrote:
read.table() does not make use of names(colClasses) - only its values.
Because of this, ordering is critical, as you noted. It shouldn't be
too hard to add support for a named `colClasses` argument of
utils::read.table(), but someone needs to convince the R core team
that this is a good idea.
As an alternative, see R.filesets::readDataFrame() for a
read.table()-like function that matches names(colClasses) to column
names, if they exists.
/Henrik
(author of R.filesets)
On Wed, Jul 8, 2015 at 5:41 PM, Andreas Leha
andreas.l...@med.uni-goettingen.de wrote:
Hi all,
Apparently, the colClasses argument to read.table needs to be in the
order of the columns *even when it is named*. Why is that? And where
would I find it in the documentation?
Here is a MWE:
--8---cut here---start-8---
kkk - c(a\tb,
3.14\tx)
read.table(textConnection(kkk),
sep=\t,
header = TRUE)
cclasses=c(b=character,
a=numeric)
read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = cclasses) ## --- error
read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = cclasses[order(names(cclasses))])
--8---cut here---end---8---
Thanks,
Andreas
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[R] tcltk2 entry box
Is anyone familiar enough with the tcltk2 package to know if it is possible to have an entry box where a user can enter information (such as a path to a file or a number) and then be able to use the entered information downstream in a R script ? The idea is for someone unfamiliar with R to just start an R script that would take care of all the commands for them so all they have to do is get the script started. However, there is always a couple of pieces of information that will change each time the script is used (for example, a different file will be processed by the script). So, I would like a way for the user to input that information as the script ran. Matthew McCormack __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] tcltk2 entry box
Dear Matthew, For file selection, see ?tcltk::tk_choose.files or ?tcltk::tkgetOpenFile . You could enter a number in a tk entry widget, but, depending upon the nature of the number, a slider or other widget might be a better choice. For a variety of helpful tcltk examples see http://www.sciviews.org/_rgui/tcltk/, originally by James Wettenhall but now maintained by Philippe Grosjean (the author of the tcltk2 package). (You probably don't need tcltk2 for the simple operations that you mention, but see ?tk2spinbox for an alternative to a slider.) Best, John --- John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.socsci.mcmaster.ca/jfox/ -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Matthew Sent: July-08-15 8:01 PM To: r-help Subject: [R] tcltk2 entry box Is anyone familiar enough with the tcltk2 package to know if it is possible to have an entry box where a user can enter information (such as a path to a file or a number) and then be able to use the entered information downstream in a R script ? The idea is for someone unfamiliar with R to just start an R script that would take care of all the commands for them so all they have to do is get the script started. However, there is always a couple of pieces of information that will change each time the script is used (for example, a different file will be processed by the script). So, I would like a way for the user to input that information as the script ran. Matthew McCormack __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 must a named colClasses in read.table be in correct order
Hi Henrik, Thanks for your reply. I am not (yet) convinced, though. The help page for read.table mentions named colClasses and if I specify colClasses for not all columns, the names are taken into account: --8---cut here---start-8--- kkk - c(a\tb, 3.14\tx) str(read.table(textConnection(kkk), sep=\t, header = TRUE)) str(read.table(textConnection(kkk), sep=\t, header = TRUE, colClasses=c(b=character))) --8---cut here---end---8--- What am I missing? Best, Andreas On 09/07/2015 02:21, Henrik Bengtsson wrote: read.table() does not make use of names(colClasses) - only its values. Because of this, ordering is critical, as you noted. It shouldn't be too hard to add support for a named `colClasses` argument of utils::read.table(), but someone needs to convince the R core team that this is a good idea. As an alternative, see R.filesets::readDataFrame() for a read.table()-like function that matches names(colClasses) to column names, if they exists. /Henrik (author of R.filesets) On Wed, Jul 8, 2015 at 5:41 PM, Andreas Leha andreas.l...@med.uni-goettingen.de wrote: Hi all, Apparently, the colClasses argument to read.table needs to be in the order of the columns *even when it is named*. Why is that? And where would I find it in the documentation? Here is a MWE: --8---cut here---start-8--- kkk - c(a\tb, 3.14\tx) read.table(textConnection(kkk), sep=\t, header = TRUE) cclasses=c(b=character, a=numeric) read.table(textConnection(kkk), sep=\t, header = TRUE, colClasses = cclasses) ## --- error read.table(textConnection(kkk), sep=\t, header = TRUE, colClasses = cclasses[order(names(cclasses))]) --8---cut here---end---8--- Thanks, Andreas __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
Hi Luigi str(my.data) 'data.frame': 540 obs. of 4 variables: $ Line : chr 1 2 3 4 ... $ Well : chr 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: chr 0.728 0.735 0.749 0.758 ... You didnot create the data.frame properly mydata - data.frame(Line=Line, Well=Well, Target=Target, Rn=Rn,Cycle= Cycle) str(mydata) 'data.frame': 540 obs. of 4 variables: $ Line : num 1 2 3 4 5 6 7 8 9 10 ... $ Well : num 1 1 1 1 1 1 1 1 1 1 ... $ Target: chr alpha alpha alpha alpha ... $ Rn: num 0.728 0.735 0.749 0.758 0.77 0.778 0.78 0.784 0.786 0.785 ... I was having problems with your script so I started with the basics (before I found the problem with the df) xyplot(Rn ~ Cycle | sprintf(%2d,Well), data = mydata, as.table = TRUE, layout = c(6,2), groups = Well) You are not splitting up the data with groups being the same as the conditioning. It can be necessary to use this setup in some cases but not this. latticeExtra is on Cran so you can use install.packages(latticeExtra) or use the menu I have never heard of lattice_Extra mydata$rown - ifelse(mydata$Well6,2,1) mydata$welln - rep(1:6, 2)[sapply(mydata$Well, pmatch, 1:12)] useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75)), xyplot(Rn ~ Cycle | welln*rown, data = mydata, as.table = TRUE, layout = c(6,2) ) ) ## useOuterStrips ps.Colours - c(#00,#FF,#00FF00,#FF,#FFA54F, #00,#FF00FF,#C0,#00B414,#FFD18F, #00B2EE,#ffe5cc,#6A5ACD,#C0C0C0,#CC, #6495ED,#FFFAFA) useOuterStrips(strip = strip.custom(factor.levels = paste(column,1:6), par.strip.text = list(cex = 0.75)), strip.left = strip.custom(factor.levels = paste(row, 1:2), horizontal = FALSE, par.strip.text = list(cex = 0.75)), xyplot(Rn ~ Cycle | welln*rown, data = mydata, as.table = TRUE, groups = Well, col = ps.Colours, layout = c(6,2) ) ) ## useOuterStrips Duncan -Original Message- From: Luigi Marongiu [mailto:marongiu.lu...@gmail.com] Sent: Thursday, 9 July 2015 09:22 To: Duncan Mackay; Dennis Murphy; r-help Subject: Re: [R] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice) In relation to this question I have prepared a workable example. First I prepare a dataframe with three variables (Cycle, Target, Rn), then I plot the results with lattice's xyplot(). I won't use the scales but only the labels and the panels are NOT indicated by the variable Well. What I would need to use are instead the vectors row.name and col.name that can identify each column and row of the plot. Secondly I create replicates of the row.name and col.name in order to fit the data and create a second dataframe, then I plot using lattice extra's useOuterStrips(). However (a) I think the call is wrong anyway, (b) I obtain Error: length(dimx) == 2 is not TRUE (c) I need a package on top of lattice (d) I might introduce errors during the creation of the second dataframe. The requirements remains to create a strip on the top and left side of the plot to allocate the elements of row.name and col.name possibly using lattice only. Thank you for your help. Luigi Line-c(1,2,3,4,5,6,7,8,9,10, 11,12,13,14,15,16,17,18,19,20, 21,22,23,24,25,26,27,28,29,30, 31,32,33,34,35,36,37,38,39,40, 41,42,43,44,45,46,47,48,49,50, 51,52,53,54,55,56,57,58,59,60, 61,62,63,64,65,66,67,68,69,70, 71,72,73,74,75,76,77,78,79,80, 81,82,83,84,85,86,87,88,89,90, 91,92,93,94,95,96,97,98,99,100, 101,102,103,104,105,106,107,108,109, 110,111,112,113,114,115,116,117,118, 119,120,121,122,123,124,125,126,127, 128,129,130,131,132,133,134,135, 136,137,138,139,140,141,142,143,144, 145,146,147,148,149,150,151,152,153, 154,155,156,157,158,159,160,161,162, 163,164,165,166,167,168,169,170, 171,172,173,174,175,176,177,178,
Re: [R] why must a named colClasses in read.table be in correct order
Hi Henrik,
Thank you very much for looking into this. And thanks for the patch!
Yes, let's hope this is a typo that gets fixed.
Regards,
Andreas
Henrik Bengtsson henrik.bengts...@ucsf.edu writes:
Thanks for insisting; I was wrong and I'm happy to see that there is
indeed code intended for named 'colClasses', which even goes back to
2004. But as you report, then names only work when
length(colClasses) cols (which also explains why I though it was not
supported). I'm not sure if that _strictly less than_ test is
intentional or a mistake, but I would propose the following patch:
[HB-X201]{hb}: svn diff src\library\utils\R\readtable.R
Index: src/library/utils/R/readtable.R
===
--- src/library/utils/R/readtable.R (revision 68642)
+++ src/library/utils/R/readtable.R (working copy)
@@ -139,7 +139,7 @@
if (rlabp) col.names - c(row.names, col.names)
nmColClasses - names(colClasses)
-if(length(colClasses) cols)
+if(length(colClasses) = cols)
if(is.null(nmColClasses)) {
colClasses - rep_len(colClasses, cols)
} else {
Your example works with this patch. I've made it source():able so you
can try it out (if you cannot source() https://, then download the
file an source it locally):
source(https://gist.githubusercontent.com/HenrikBengtsson/ed1eeb41a1b4d6c43b47/raw/ebe58f76e518dd014423bea466a5c93d2efd3c99/readtable-fix.R;)
kkk - c(a\tb,
3.14\tx)
colClasses - c(a=numeric, b=character)
data - read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = colClasses)
str(data)
### 'data.frame': 1 obs. of 2 variables:
### $ a: num 3.14
### $ b: chr x
## Does not work with utils::read.table(), but with patch
data - read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = rev(colClasses))
str(data)
### 'data.frame': 1 obs. of 2 variables:
### $ a: num 3.14
### $ b: chr x
Let's hope that the above is a (10-year old) typo, and changing a to
a = adds support for named 'colClasses', which is a really useful
functionality.
/Henrik
On Wed, Jul 8, 2015 at 6:42 PM, Andreas Leha
andreas.l...@med.uni-goettingen.de wrote:
Hi Henrik,
Thanks for your reply.
I am not (yet) convinced, though. The help page for read.table
mentions named colClasses and if I specify colClasses for not all
columns, the names are taken into account:
--8---cut here---start-8---
kkk - c(a\tb,
3.14\tx)
str(read.table(textConnection(kkk),
sep=\t,
header = TRUE))
str(read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses=c(b=character)))
--8---cut here---end---8---
What am I missing?
Best,
Andreas
On 09/07/2015 02:21, Henrik Bengtsson wrote:
read.table() does not make use of names(colClasses) - only its values.
Because of this, ordering is critical, as you noted. It shouldn't be
too hard to add support for a named `colClasses` argument of
utils::read.table(), but someone needs to convince the R core team
that this is a good idea.
As an alternative, see R.filesets::readDataFrame() for a
read.table()-like function that matches names(colClasses) to column
names, if they exists.
/Henrik
(author of R.filesets)
On Wed, Jul 8, 2015 at 5:41 PM, Andreas Leha
andreas.l...@med.uni-goettingen.de wrote:
Hi all,
Apparently, the colClasses argument to read.table needs to be in the
order of the columns *even when it is named*. Why is that? And where
would I find it in the documentation?
Here is a MWE:
--8---cut here---start-8---
kkk - c(a\tb,
3.14\tx)
read.table(textConnection(kkk),
sep=\t,
header = TRUE)
cclasses=c(b=character,
a=numeric)
read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = cclasses) ## --- error
read.table(textConnection(kkk),
sep=\t,
header = TRUE,
colClasses = cclasses[order(names(cclasses))])
--8---cut here---end---8---
Thanks,
Andreas
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[R] Para r-help
Tudo bem? Sou a Josie, achei voc� na internet e queria aproveitar para fazer o marketing do site onde estou trabalhando ;) Pra mim � o melhor lugar para fazer amigos, achar um relacionamento e at� um encontro assim... mais �ntimo. O link � este: http://goo.gl/DWtKBg (N�o se preocupe, n�o � v�rus! Juro!) Estou cadastrada l� como josymel. Cadastre-se tamb�m para conversamos por l�. Desculpa te mandar um email assim sem permiss�o ok? Te encontro l�! Bjs!!! Josie [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] add outer strip for levels in lattice plot (useOuterStrips alternative for Lattice)
In relation to this question I have prepared a workable example. First I prepare a dataframe with three variables (Cycle, Target, Rn), then I plot the results with lattice's xyplot(). I won't use the scales but only the labels and the panels are NOT indicated by the variable Well. What I would need to use are instead the vectors row.name and col.name that can identify each column and row of the plot. Secondly I create replicates of the row.name and col.name in order to fit the data and create a second dataframe, then I plot using lattice extra's useOuterStrips(). However (a) I think the call is wrong anyway, (b) I obtain Error: length(dimx) == 2 is not TRUE (c) I need a package on top of lattice (d) I might introduce errors during the creation of the second dataframe. The requirements remains to create a strip on the top and left side of the plot to allocate the elements of row.name and col.name possibly using lattice only. Thank you for your help. Luigi Line-c(1,2,3,4,5,6,7,8,9,10, 11,12,13,14,15,16,17,18,19,20, 21,22,23,24,25,26,27,28,29,30, 31,32,33,34,35,36,37,38,39,40, 41,42,43,44,45,46,47,48,49,50, 51,52,53,54,55,56,57,58,59,60, 61,62,63,64,65,66,67,68,69,70, 71,72,73,74,75,76,77,78,79,80, 81,82,83,84,85,86,87,88,89,90, 91,92,93,94,95,96,97,98,99,100, 101,102,103,104,105,106,107,108,109, 110,111,112,113,114,115,116,117,118, 119,120,121,122,123,124,125,126,127, 128,129,130,131,132,133,134,135, 136,137,138,139,140,141,142,143,144, 145,146,147,148,149,150,151,152,153, 154,155,156,157,158,159,160,161,162, 163,164,165,166,167,168,169,170, 171,172,173,174,175,176,177,178,179, 180,181,182,183,184,185,186,187,188, 189,190,191,192,193,194,195,196,197, 198,199,200,201,202,203,204,205, 206,207,208,209,210,211,212,213,214, 215,216,217,218,219,220,221,222,223, 224,225,226,227,228,229,230,231,232, 233,234,235,236,237,238,239,240, 241,242,243,244,245,246,247,248,249, 250,251,252,253,254,255,256,257,258, 259,260,261,262,263,264,265,266,267, 268,269,270,271,272,273,274,275, 276,277,278,279,280,281,282,283,284, 285,286,287,288,289,290,291,292,293, 294,295,296,297,298,299,300,301,302, 303,304,305,306,307,308,309,310, 311,312,313,314,315,316,317,318,319, 320,321,322,323,324,325,326,327,328, 329,330,331,332,333,334,335,336,337, 338,339,340,341,342,343,344,345, 346,347,348,349,350,351,352,353,354, 355,356,357,358,359,360,361,362,363, 364,365,366,367,368,369,370,371,372, 373,374,375,376,377,378,379,380, 381,382,383,384,385,386,387,388,389, 390,391,392,393,394,395,396,397,398, 399,400,401,402,403,404,405,406,407, 408,409,410,411,412,413,414,415, 416,417,418,419,420,421,422,423,424, 425,426,427,428,429,430,431,432,433, 434,435,436,437,438,439,440,441,442, 443,444,445,446,447,448,449,450, 451,452,453,454,455,456,457,458,459, 460,461,462,463,464,465,466,467,468, 469,470,471,472,473,474,475,476,477, 478,479,480,481,482,483,484,485, 486,487,488,489,490,491,492,493,494, 495,496,497,498,499,500,501,502,503, 504,505,506,507,508,509,510,511,512, 513,514,515,516,517,518,519,520, 521,522,523,524,525,526,527,528,
[R] clm funtion and CI
Hi, I'm working with ordinal logistic regression and fitting the model with the clm funtion of the ordinal package and would like to get the CI. According to the Tutorial on fitting Cumulative Link Models with the ordinal Package, Rune Haubo B Christensen (21 January 2015) you can run the OR, but not CI. The same happens with the clm2 for partial proportional odds. I appreciate any help !! Luciane __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 must a named colClasses in read.table be in correct order
Hi all, Apparently, the colClasses argument to read.table needs to be in the order of the columns *even when it is named*. Why is that? And where would I find it in the documentation? Here is a MWE: --8---cut here---start-8--- kkk - c(a\tb, 3.14\tx) read.table(textConnection(kkk), sep=\t, header = TRUE) cclasses=c(b=character, a=numeric) read.table(textConnection(kkk), sep=\t, header = TRUE, colClasses = cclasses) ## --- error read.table(textConnection(kkk), sep=\t, header = TRUE, colClasses = cclasses[order(names(cclasses))]) --8---cut here---end---8--- Thanks, Andreas __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] tcltk2 entry box
Wow ! Very nice. Thank you very much, John. This is very helpful and just what I need. Yes, I can see that I should have paid attention to tcltk before going to tcltk2. Matthew On 7/8/2015 8:37 PM, John Fox wrote: Dear Matthew, For file selection, see ?tcltk::tk_choose.files or ?tcltk::tkgetOpenFile . You could enter a number in a tk entry widget, but, depending upon the nature of the number, a slider or other widget might be a better choice. For a variety of helpful tcltk examples see http://www.sciviews.org/_rgui/tcltk/, originally by James Wettenhall but now maintained by Philippe Grosjean (the author of the tcltk2 package). (You probably don't need tcltk2 for the simple operations that you mention, but see ?tk2spinbox for an alternative to a slider.) Best, John --- John Fox, Professor McMaster University Hamilton, Ontario, Canada http://socserv.socsci.mcmaster.ca/jfox/ -Original Message- From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Matthew Sent: July-08-15 8:01 PM To: r-help Subject: [R] tcltk2 entry box Is anyone familiar enough with the tcltk2 package to know if it is possible to have an entry box where a user can enter information (such as a path to a file or a number) and then be able to use the entered information downstream in a R script ? The idea is for someone unfamiliar with R to just start an R script that would take care of all the commands for them so all they have to do is get the script started. However, there is always a couple of pieces of information that will change each time the script is used (for example, a different file will be processed by the script). So, I would like a way for the user to input that information as the script ran. Matthew McCormack __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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 email has been checked for viruses by Avast antivirus software. https://www.avast.com/antivirus __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/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] problem understanding grid coordinate systems
According to R Graphics by Paul Murrell, the coordinates that were used for the most recent lattics plot can be retrieved with native units. I have difficulties to access these coordinates. The following code renders the following results: library(grid) library(lattice) pl - xyplot(1:10 ~ 10:1) print(pl) convertX(unit(.9, npc), native) [1] 605.7native R.version _ platform i686-pc-linux-gnu arch i686 os linux-gnu system i686, linux-gnu status major 3 minor 0.2 year 2013 month 09 day25 svn rev63987 language R version.string R version 3.0.2 (2013-09-25) nickname Frisbee Sailing I had expected something around 9.5 in native coordinates. Which coordinate system do I have to address instead? -- Johannes Hüsing __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
