Re: [R] shift by one column given rows in a dataframe
hi thank you all for the great replies, very useful indeed even if some of them a bit too aggressive (which is never, ever a good approach in my very humble opinion... but that's a matter of taste and style I do not want to discuss here); sorry again for bothering someone with such a trivial and ill-conceived question finally, I'm posting here my solution as a reference to the problem so that to close this long and winding thread; hoping this code might be somehow useful for someonelse, sometime, somewhere... ## start code v0-c(a,xxx,c,rep(xxx,2)) v1-c(1,b,3,d,e) v2-c(6,2,8,4,5) v3-c(xxx,7,xxx,9,10) df_start-data.frame(v0,v1,v2,v3, stringsAsFactors = FALSE) df_start # set vector of rows to be shifted left shIftLeft-c(2,4,5) # shift selected rows df_start[shIftLeft,1:3]-df_start[shIftLeft,2:4] # final result df_end-df_start[,1:3] df_end ## end code thanks -- View this message in context: http://r.789695.n4.nabble.com/shift-by-one-column-given-rows-in-a-dataframe-tp4710256p4710294.html Sent from the R help mailing list archive at Nabble.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] R GUI plot by color
Hi, I want to do a plot from a variable (which i select from a listbox) with the color factor of the variable that i have selected from another listbox. To be not very heavy pasting all the code, i will only paste real important parts: data1 and data2 are the extacted parts of the dataframes data from a tcltk listbox: data1- dataframe[as.numeric(tkcurselection(tl))+1] data2- dataframe[as.numeric(tkcurselection(tl))+1] As i want to plot the data1 with the color of data2, i use this code: plot(data1,col=colnames(data2)) This works perfect for plotting the data1 variable, but it do not change the col of the dots by data2. I also have probed with plot(data1,col=factor(colnames(data2))) But nothing happens with the color. Thanks!! -- View this message in context: http://r.789695.n4.nabble.com/R-GUI-plot-by-color-tp4710297.html Sent from the R help mailing list archive at Nabble.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] Table Looks Funny
Hi Marissa, Unfortunately we didn't get the picture. If you want to send an image, PDF is probably your best bet. If that is not possible, perhaps a description of the weirdness that has confronted you will allow someone to suggest a solution. Jim On Fri, Jul 24, 2015 at 7:08 AM, Marissa Fahlberg marissa.fahlb...@gmail.com wrote: Hey, I can't seem to import my csv file in such a way that the table looks normal. The dimensions are correct, 4x7, and I set my header =TRUE, but it still looks weird. Attached is the picture. Any ideas?? Thanks!! -Marissa __ 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] R GUI plot by color
Hi jpara3, Hmmm. It's becoming clearer, yes I think the answer is emerging from the swirling clouds of uncertainty. 1) The column names of data2 are not numbers 2) The number of columns in data2 is not equal to the number of values in data1 that you are plotting 3) You probably want to plot colors determined by the values in data2, not the names of its columns Please send payment for this psychic reading to Jim On Fri, Jul 24, 2015 at 6:43 PM, jpara3 j.para.fernan...@hotmail.com wrote: Hi, I want to do a plot from a variable (which i select from a listbox) with the color factor of the variable that i have selected from another listbox. To be not very heavy pasting all the code, i will only paste real important parts: data1 and data2 are the extacted parts of the dataframes data from a tcltk listbox: data1- dataframe[as.numeric(tkcurselection(tl))+1] data2- dataframe[as.numeric(tkcurselection(tl))+1] As i want to plot the data1 with the color of data2, i use this code: plot(data1,col=colnames(data2)) This works perfect for plotting the data1 variable, but it do not change the col of the dots by data2. I also have probed with plot(data1,col=factor(colnames(data2))) But nothing happens with the color. Thanks!! -- View this message in context: http://r.789695.n4.nabble.com/R-GUI-plot-by-color-tp4710297.html Sent from the R help mailing list archive at Nabble.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-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 GUI plot by color
I have done a trial with a dataframe like this: one-c(3,2,2) two-c(a,b,b) data-dataframe(uno,dos) plot(data$one,col=data$two) and it plots perfect. If I try it with the code that i have post in the first message, selecting data1 and data2 as i nthis example, the plot is plotted, but all dots with the same color. Thanks for the answer but noone of the 3 topics is the root problem. -- View this message in context: http://r.789695.n4.nabble.com/R-GUI-plot-by-color-tp4710297p4710300.html Sent from the R help mailing list archive at Nabble.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] how to install and use Rcplex package
Hello, Try install.packages(Rcplex) That's it. Hope this helps, Rui Barradas Em 24-07-2015 12:20, Yasin Gocgun escreveu: Hi, I need to know how to completely install Rcplex to be able to use cplex in R. According to the instructions given in the following webpage, I edited the Makevars.win file: https://cran.r-project.org/web/packages/Rcplex/INSTALL The revised Makevars.win file includes only the following lines: PKG_CPPFLAGS=-I/C:/ilog/CPLEX_Studio122/include PKG_LIBS=-L/C:/ilog/CPLEX_Studio122/cplex/lib/x64_windows_vs2008/stat_mda-lcplex122 -lm First, I am not sure whether the above lines are completely correct. Second, I don'y know what is the next step in installing and using Rcplex. So can someone help me about this issue? Thank you in advance, __ 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 calculate the average direct effect, average total effect and average indirect effect for spatial regression models with spatial lag of dependent variable
Hello, the command impacts in the spdep-packeage should help you. Mit freundlichen Grüßen Linus Holtermann Hamburgisches WeltWirtschaftsInstitut gemeinnützige GmbH (HWWI) Heimhuder Straße 71 20148 Hamburg Tel +49-(0)40-340576-336 Fax+49-(0)40-340576-776 Internet: www.hwwi.org Email: holterm...@hwwi.org Amtsgericht Hamburg HRB 94303 Geschäftsführer: PD Dr. Christian Growitsch | Prof. Dr. Henning Vöpel Prokura: Dipl. Kauffrau Alexis Malchin Umsatzsteuer-ID: DE 241849425 -Ursprüngliche Nachricht- Von: R-help [mailto:r-help-boun...@r-project.org] Im Auftrag von wenyueyang Gesendet: Donnerstag, 23. Juli 2015 17:35 An: r-help@r-project.org Betreff: [R] How to calculate the average direct effect, average total effect and average indirect effect for spatial regression models with spatial lag of dependent variable Hi, I am using four spatial regression models (SAR, SEM, SAC and SDM) to evaluate the spillover effect of some factors. LeSage and Pace (2009) pointed out that when the spatial lag of the dependent variable is included in the model, parameter estimates lose their conventional interpretation as marginal effects, because the spatial lag gives rise to a series of feedback loops and spillover effects across regions. Therefore, I need to calculate the three different marginal effects: average direct effect, average total effect and average indirect (spillover) effect, and this is what I don't know how to perform in R. Can you teach me about how to calculate the average direct effect, average total effect and average indirect (spillover) effect for the spatial regression models in R and tell me the related R code? I would like to express my great appreciation to you! Thank you very much and best regards. Yours sincerely, Wenyue Yang -- View this message in context: http://r.789695.n4.nabble.com/How-to-calculate-the-average-direct-effect-average-total-effect-and-average-indirect-effect-for-spate-tp4710253.html Sent from the R help mailing list archive at Nabble.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-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] how to install and use Rcplex package
Hi, I need to know how to completely install Rcplex to be able to use cplex in R. According to the instructions given in the following webpage, I edited the Makevars.win file: https://cran.r-project.org/web/packages/Rcplex/INSTALL The revised Makevars.win file includes only the following lines: PKG_CPPFLAGS=-I/C:/ilog/CPLEX_Studio122/include PKG_LIBS=-L/C:/ilog/CPLEX_Studio122/cplex/lib/x64_windows_vs2008/stat_mda-lcplex122 -lm First, I am not sure whether the above lines are completely correct. Second, I don'y know what is the next step in installing and using Rcplex. So can someone help me about this issue? Thank you in advance, -- Yasin Gocgun __ 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 GUI plot by color
Hi jpara3, Your example, when I got it to go: one-c(3,2,2) two-c(a,b,b) data-dataframe(one,two) plot(data$one,col=data$two) does indeed work, and I'll explain how. You are plotting the values of data$one against the _values_ of data$two (see point 3 of my response). In this case, the values of data$two are of class factor, which means that they have numeric values attached to the levels (a, b) of the factor. When you pass these values as the col argument, they are silently converted to their numeric values (1,2,2). In the default palette, these numbers represent the colors - black, red, red. Those are the colors in which the points are plotted. So far, so good. Let's look at the other two points that I guessed. 1) The column names of data2 are not numbers colnames(data) [1] one two As you can see, the column names are character variables, and they don't translate to numbers: as.numeric(colnames(data)) [1] NA NA 2) The number of columns in data2 is not equal to the number of values in data1 that you are plotting It's pretty obvious that there are two values in the column names and three in the vector of values that you are plotting in your example.So, I think I got three out of three without knowing what the data were. Jim On Fri, Jul 24, 2015 at 7:53 PM, jpara3 j.para.fernan...@hotmail.com wrote: I have done a trial with a dataframe like this: one-c(3,2,2) two-c(a,b,b) data-dataframe(uno,dos) plot(data$one,col=data$two) and it plots perfect. If I try it with the code that i have post in the first message, selecting data1 and data2 as i nthis example, the plot is plotted, but all dots with the same color. Thanks for the answer but noone of the 3 topics is the root problem. -- View this message in context: http://r.789695.n4.nabble.com/R-GUI-plot-by-color-tp4710297p4710300.html Sent from the R help mailing list archive at Nabble.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-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] Which is the best way of reporting results of lme() in two different possible cases?
Dear List Memebers, I need some advise about how to report the output of lme(). When searching for correlations between between a dependent variable and a factor or a combination of factors in a repeated measure design with lme() I noticed that I can encounter two types of results, and I am wondering which is the best way to report each of them in a journal publication. It is not clear to me when I should report the values of the beta coefficient together with the t-test value and p-value, or the beta coefficient with F value and p-value. Let’s have as a reference the following two models: MODEL TYPE 1: fixed effects only lme_Weigth - lme(Sound_Feature ~ Weight, data = My_Data, random = ~1 | Subject) summary(lme_Weigth) lme_Height - lme(Sound_Feature ~ Height, data = My_Data, random = ~1 | Subject) summary(lme_Height) MODEL TYPE 2: Fixed and interaction effects together lme_Interaction - lme(Sound_Feature ~ Weight*Height, data = My_Data, random = ~1 | Subject) summary(lme_Interaction) anova.lme(lme_Interaction, type = marginal). RESULTS CASE 1: Applying model type 2 I do not get any significant p-value so there is no interaction effect. Therefore I check the simplified model type 1, and I get for both Height and Weight significant p-values. RESULTS CASE 2: Applying model type 2 I get a significant p-value so there is an interaction effect. Therefore I do not check the simplified model type 1 for the two factors separately. Moreover, in the results of model type 2 I can also see that the fixed effects of both factors are significant. I am not sure if in presence of an interaction it is correct to report the significant interactions of the separate factors, since I read somewhere that it does not make too much sense. Am I wrong? My attempt in reporting the results for the two cases is the following. Can you please tell me it I am right? “We performed a linear mixed effects analysis of the relationship between Sound_Feature and Height and Weight. As fixed effects, we entered Height and Weight (without interaction term) into a first model, and we included the interaction effect into a second model. As random effects, we had intercepts for subjects.” RESULTS CASE 1: “Results showed that Sound_Feature was linearly related to Height (beta = value, t(df)= value, p 0.05) and Weight (beta = value, t(df)= value, p 0.05), but no to their interaction effect.” RESULTS CASE 2: “Results showed that Sound_Feature was linearly related to Height (beta = value, F(df)= value, p 0.05) and Weight (beta = value, F(df)= value, p 0.05), and to their interaction effect (beta = value, F(df)= value, p 0.05).” Basically I used for reporting the beta value in the 2 cases I use the output of summary(). In the case 1, I report the value of the t-test, still taken from summary. But for case 2 I do not report the t-test, I report the F value as result of anova.lme(lme_Interaction, type = marginal). Is this the correct way of proceeding in the results reporting? I give an example of the outputs I get using the two models for the three cases: RESULTS CASE 1: ### Sound_Level_Peak vs Weight*Height ### library(nlme) lme_Sound_Level_Peak - lme(Sound_Level_Peak ~ Weight*Height, data = My_Data1, random = ~1 | Subject) summary(lme_Sound_Level_Peak) Linear mixed-effects model fit by REML Data: My_Data1 AIC BIClogLik 716.2123 732.4152 -352.1061 Random effects: Formula: ~1 | Subject (Intercept) Residual StdDev:5.470027 4.246533 Fixed effects: Sound_Level_Peak ~ Weight * Height Value Std.Error DFt-value p-value (Intercept) -7.185833 97.56924 95 -0.0736485 0.9414 Weight 0.993543 1.63151 15 0.6089715 0.5517 Height-0.076300 0.55955 15 -0.1363592 0.8934 Weight:Height -0.005403 0.00898 15 -0.6017421 0.5563 Correlation: (Intr) Weight Height Weight-0.927 Height-0.994 0.886 Weight:Height 0.951 -0.996 -0.919 Standardized Within-Group Residuals: Min Q1 Med Q3 Max -2.95289464 -0.51041805 -0.06414148 0.48562230 2.95415889 Number of Observations: 114 Number of Groups: 19 anova.lme(lme_Sound_Level_Peak,type = marginal) numDF denDF F-value p-value (Intercept) 195 0.0054241 0.9414 Weight115 0.3708463 0.5517 Height115 0.0185938 0.8934 Weight:Height 115 0.3620936 0.5563 ### Sound_Level_Peak vs Weight ### library(nlme) summary(lme(Sound_Level_Peak ~ Weight, data = My_Data1, random = ~1 | Subject)) Linear mixed-effects model fit by REML Data: My_Data1 AIC BIClogLik 706.8101 717.6841 -349.4051 Random effects: Formula: ~1 | Subject (Intercept) Residual StdDev:5.717712 4.246533 Fixed effects: Sound_Level_Peak ~ Weight
Re: [R] how to install and use Rcplex package
It's important to look at the CRAN documentation, where it is quite clear there are NO Windows binaries for this package. My suggestion -- set up the (freeware) VirtualBox or a similar Virtual Machine environment, install a Linux OS virtually, and install there. If there is no Windows binary on CRAN, there is likely a very good reason. You may actually find that something like Lubuntu or Linux Mint are more convenient for working with R. JN On 15-07-24 09:54 AM, Yasin Gocgun wrote: Hi, Thanks for your email. When I use that line, I received the following messages from R: package ‘Rcplex’ is available as a source package but not as a binary package ‘Rcplex’ is not available (for R version 3.1.1) So, do you see what the problem is? Thank you, Yasin On Fri, Jul 24, 2015 at 4:04 PM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, Try install.packages(Rcplex) That's it. Hope this helps, Rui Barradas Em 24-07-2015 12:20, Yasin Gocgun escreveu: Hi, I need to know how to completely install Rcplex to be able to use cplex in R. According to the instructions given in the following webpage, I edited the Makevars.win file: https://cran.r-project.org/web/packages/Rcplex/INSTALL The revised Makevars.win file includes only the following lines: PKG_CPPFLAGS=-I/C:/ilog/CPLEX_Studio122/include PKG_LIBS=-L/C:/ilog/CPLEX_Studio122/cplex/lib/x64_windows_vs2008/stat_mda-lcplex122 -lm First, I am not sure whether the above lines are completely correct. Second, I don'y know what is the next step in installing and using Rcplex. So can someone help me about this issue? Thank you in advance, __ 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 version update
On Jul 21, 2015, at 11:55 AM, kle...@sxmail.de wrote: Dear Ladies and Gentlemen, as a beginner in R, I encountered a sort of naturally given limitsconcerning the process of amending R with packages. I apparently own version 3.0.2 and I principally decided to use R via the RKWard GUI on Linux Kubuntu Trusty Tahr; the R version installed on my computer is admittedly not far from the basics provided by my distribution's package management (also throughout multiple rounds of updates/ upgrades of the system). What would I have to do to finally update/ upgrade beyond that R version? Would that process (generally?) affect any/ my GUI? This problem appeared to me as I was busy installing packages an received the error message package ‘ATLAS’ is not available (for R version 3.0.2) . ATLAS is not an R package: https://launchpad.net/ubuntu/+source/atlas I am quite desperate and would look forward to be indicated a path to a sustainable solution or be told how to mitigate/ circumvent (these/ such) problems. Thanks a lot! Best regards,Markus Hofstetter [[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. David Winsemius Alameda, CA, USA __ 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] Infinite Series
Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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] R version update
Hi Markus, Please keep the list copied. See responses in line. On Fri, Jul 24, 2015 at 1:22 PM, kle...@sxmail.de wrote: Dear Ista Zahn, Thank you that you answered. Kubuntu delivered some packages of R and I obviously got R version 3.0.2 by the time (early 2015) I installed R fully on my Linux Kubuntu Trusty Tahr. Yes, I understood that much. If you want to upgrade to a more recent version follow the instructions in the first link I sent you last time (https://cran.r-project.org/bin/linux/ubuntu/). The package ATLAS is a recommended one from recent R-explaining literature that I intend to work through to get accustomed and tackle R as fully as I can. Well, AFAIK there is no such package on CRAN. What literature exactly are you referring to? I had to experience that beyond a package called ATLAS a certain number of further other very useful packages were not available because being not for R version 3.0.2 as I appended when speaking of the problem ATLAS. My conclusion up to now is: I cannot use R fully because I have no opportunity to update my basic R version AS SUCH. I hope there is a way of solving this without destroying too much of the wealth of packages I have already integrated. OK, so follow the instructions for updating. Best, ISta Best regards, Markus Hofstetter Ista Zahn istaz...@gmail.com schrieb (22.07.2015 14:24): On Jul 21, 2015 9:30 PM, kle...@sxmail.de wrote: Dear Ladies and Gentlemen, as a beginner in R, I encountered a sort of naturally given limitsconcerning the process of amending R with packages. I apparently own version 3.0.2 and I principally decided to use R via the RKWard GUI on Linux Kubuntu Trusty Tahr; the R version installed on my computer is admittedly not far from the basics provided by my distribution's package management (also throughout multiple rounds of updates/ upgrades of the system). What would I have to do to finally update/ upgrade beyond that R version? https://cran.r-project.org/bin/linux/ubuntu/ Would that process (generally?) affect any/ my GUI? possibly. This problem appeared to me as I was busy installing packages an received the error message package ‘ATLAS’ is not available (for R version 3.0.2) . I don't think there is any package on CRAN with that name. What makes you think there is? I am quite desperate and would look forward to be indicated a path to a sustainable solution or be told how to mitigate/ circumvent (these/ such) problems. I'm not actually sure exactly what the problem is... Thanks a lot! Best regards,Markus Hofstetter [[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 simulate informative censoring in a Cox PH model?
Hi Greg
Many thanks for taking the time to respond to my query. You are right about
pointing out the distinction between what variables are and are not
included in the event times process and in the censoring process. I clearly
forgot this important aspect. I amended my code to do as you advise and now
I am indeed getting biased estimates when using the informatively censored
responses. The problem is now that the estimates from the independently
censored responses are the same - i.e. they are just as biased. Thus the
bias seems to be due entirely to model mis-specification and not the
informative censoring.
To give a concrete example I simulate event times T_i and censoring times
C_i from the following models;
T_i~ Weibull(lambda_t(x),v_t),lambda_t(x)=lambda_t*exp( beta_t_0 +
(beta_t_1*Treat_i) + (beta_t_2*Z_i) + (beta_t_3*Treat_i*Z_i) )
C_i~ Weibull(lambda_c(x),v_c),lambda_c(x)=lambda_c*exp( beta_c_0 +
(beta_c_1*Treat_i) + (beta_c_2*Z_i) + (beta_c_3*Treat_i*Z_i) )
D_i~Weibull(lambda_d(x),v_D), lambda_d(x)=lamda_d*exp( beta_d_0)
where ;
beta_t_0 = 1, beta_t_1 = -1, beta_t_2 = 1, beta_t_3 = -2, lambda_t=0.5
beta_c_0 = 0.2, beta_c_1 = -2, beta_c_2 = 2, beta_c_3 = -2,
lambda_c=0.5
beta_d_0 = -0.7, lambda_d=0.1
When I fit the cox model to both the informatively censored responses and
the independent censored responses I include only the Treatment covariate
in the model.
I simulate Treatment from a Bernoulli distribution with p=0.5 and Z_i from
a beta distribution so that Z ranges from 0 to 1 (I like to think of Z as a
poor prognosis probability where Z_i=1 means a subject is 100% certain to
have a poor prognosis and Z_i=0 means zero chance). These parameter choices
give approximately 27% and 25% censoring for the informatively censored
responses (using C_i) and the independent censored responses (using D_i)
respectively. I use N=2000 subjects and 2000 simulation replications.
The above simulation I get estimates of beta_t_2 of -1.526 and -1.537 for
the informatively censored responses and the independent censored responses
respectively.
Furthermore when I fit a cox model to the full responses (no censoring at
all) I get an estimate of beta_t_2 of -1.542. This represents the best that
can possibly be done given that Z and Treat*Z are not in the model. Clearly
censoring is not making much of a difference here - model mis-specification
dominates.
I still must be doing something wrong but I cannot figure this one out.
Thanks
Dan
On Thu, Jul 23, 2015 at 12:33 AM, Greg Snow 538...@gmail.com wrote:
I think that the Cox model still works well when the only information
in the censoring is conditional on variables in the model. What you
describe could be called non-informative conditional on x.
To really see the difference you need informative censoring that
depends on something not included in the model. One option would be
to use copulas to generate dependent data and then transform the
values using your Weibul. Or you could generate your event times and
censoring times based on x1 and x2, but then only include x1 in the
model.
On Wed, Jul 22, 2015 at 2:20 AM, Daniel Meddings dpmeddi...@gmail.com
wrote:
I wish to simulate event times where the censoring is informative, and to
compare parameter estimator quality from a Cox PH model with estimates
obtained from event times generated with non-informative censoring.
However
I am struggling to do this, and I conclude rather than a technical flaw
in
my code I instead do not understand what is meant by informative and
un-informative censoring.
My approach is to simulate an event time T dependent on a vector of
covariates x having hazard function h(t|x)=lambda*exp(beta'*x)v*t^{v-1}.
This corresponds to T~ Weibull(lambda(x),v), where the scale parameter
lambda(x)=lambda*exp(beta'*x) depends on x and the shape parameter v is
fixed. I have N subjects where T_{i}~ Weibull(lambda(x_{i}),v_{T}),
lambda(x_{i})=lambda_{T}*exp(beta_{T}'*x_{i}), for i=1,...,N. Here I
assume
the regression coefficients are p-dimensional.
I generate informative censoring times C_i~ Weibull(lambda(x_i),v_C),
lambda(x_i)=lambda_C*exp(beta_C'*x_i) and compute Y_inf_i=min(T_i,C_i)
and
a censored flag delta_inf_i=1 if Y_inf_i = C_i (an observed event), and
delta_inf_i=0 if Y_inf_i C_i (informatively censored: event not
observed). I am convinced this is informative censoring because as long
as
beta_T~=0 and beta_C~=0 then for each subject the data generating process
for T and C both depend on x.
In contrast I generate non-informative censoring times
D_i~Weibull(lambda_D*exp(beta_D),v_D), and compute Y_ninf_i=min(T_i,D_i)
and a censored flag delta_ninf_i=1 if Y_ninf_i = D_i (an observed
event),
and delta_ninf_i=0 if Y_ninf_i D_i (non-informatively censored: event
not
observed). Here beta_D is a scalar. I scale the simulation by choosing
the lambda_T, lambda_C and lambda_D parameters
Re: [R] Infinite Series
Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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.
Re: [R-es] Método S3 paquete
Hola, ¿qué tal?
Sigue
http://www.datanalytics.com/2011/08/04/desarrollo-de-paquetes-con-r-iv-funciones-genericas/
a rajatabla y lo tendrás.
Un saludo,
Carlos J. Gil Bellosta
http://www.datanalytics.com
P.D.: Si te fijas bien, no estás siguiendo esa guía a rajatabla.
El día 23 de julio de 2015, 16:26, guillermo.vi...@uv.es escribió:
Hola,
Estoy tratando de crear un método S3 llamado anthr dentro del paquete
que estoy desarrollando, cuyo argumento principal es res que
básicamente es una lista con un solo componente. Pero si el segundo
argumento llamado oneSize es FALSE, res es una lista de listas.
Lo que he escrito hasta el momento es lo siguiente:
anthr - function(res, oneSize, nsizes){
UseMethod(anthr)
}
anthr.tri - function(res, oneSize, nsizes){
if(oneSize){
cases - c()
cases - res$meds
}else{
cases - list()
for (i in 1 : (nsizes - 1)){
cases[[i]] - res[[i]]$meds
}
}
return(cases)
}
El problema cuando instalo el paquete y utilizo este método, es que R no
me reconoce que res sea una lista. En concreto, me aparece este error:
Error in UseMethod(anthr) :
no applicable method for 'anthr' applied to an object of class list
He tratado de añadir esto:
tri - function(x){
value - list(meds = x$meds)
attr(value, class) - tri
value
}
pero sigue sin funcionarme. ¿Alguien puede ofrecerme alguna ayuda?.
Muchas gracias de antemano.
Un saludo,
Guillermo
___
R-help-es mailing list
R-help-es@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-help-es
___
R-help-es mailing list
R-help-es@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-help-es
Re: [R] how to install and use Rcplex package
Hi, Thanks for your email. When I use that line, I received the following messages from R: package ‘Rcplex’ is available as a source package but not as a binary package ‘Rcplex’ is not available (for R version 3.1.1) So, do you see what the problem is? Thank you, Yasin On Fri, Jul 24, 2015 at 4:04 PM, Rui Barradas ruipbarra...@sapo.pt wrote: Hello, Try install.packages(Rcplex) That's it. Hope this helps, Rui Barradas Em 24-07-2015 12:20, Yasin Gocgun escreveu: Hi, I need to know how to completely install Rcplex to be able to use cplex in R. According to the instructions given in the following webpage, I edited the Makevars.win file: https://cran.r-project.org/web/packages/Rcplex/INSTALL The revised Makevars.win file includes only the following lines: PKG_CPPFLAGS=-I/C:/ilog/CPLEX_Studio122/include PKG_LIBS=-L/C:/ilog/CPLEX_Studio122/cplex/lib/x64_windows_vs2008/stat_mda-lcplex122 -lm First, I am not sure whether the above lines are completely correct. Second, I don'y know what is the next step in installing and using Rcplex. So can someone help me about this issue? Thank you in advance, -- Yasin Gocgun __ 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 GUI plot by color
Yes, you were right!! Thanks. -- View this message in context: http://r.789695.n4.nabble.com/R-GUI-plot-by-color-tp4710297p4710320.html Sent from the R help mailing list archive at Nabble.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] Infinite Series
Janh: It sounds like you really need to go through an R tutorial or two before posting further, as this is a pretty basic query. Or am I wrong about this? An answer: Just use indexing cumsum(1/seq_len(100)^2)[seq(10, to = 100,by = 10)] ## keeps every 10th [1] 1.549768 1.596163 1.612150 1.620244 1.625133 1.628406 1.630750 1.632512 1.633884 [10] 1.634984 But beware FAQ 7.31 for long series. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Fri, Jul 24, 2015 at 4:37 PM, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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-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] “Error in if (abs(x - oldx) ftol)” when using “lognormal” distribution in mixed logit
Den 2015-07-24 kl. 00:33, skrev Dera:
Hi, I have a question about how to use the mlogit package in R to do analysis
of discrete choice survey data. Our survey is about asking people to choose
from different insurance policies(with two attributes of deductible and
premium).
The code I used to fit mixed logit is:
[1] ml - mlogit.data (mydata, choice=choice, shape = wide, id =
individual,
opposite =c ('deductible', 'premium'),varying = 5:10)
[2] ml.w5 - mlogit (choice~deductible+premium|0, ml, panel = TRUE,
rpar = c(deductible='ln', premium='ln'),
R = 100, halton = NA, print.level=0)
I try to use lognormal because we hope the coefficients for both deductible
and premium are negative. And I use opposite in [1] to reverse the sign
because lognormal is always positive.
But I always get the error warning:
Error in if (abs(x - oldx) ftol) { : missing value where TRUE/FALSE
needed
In addition: Warning message: In log(start[ln]) : NaNs produced
I double check the data and am sure there isn't any missing data. And if I
change the lognormal ln to n or cn, it will work without any warning.
Does anyone know how to deal with this? Thank you for your help.
I've never used the 'mlogit' package but that error message has likely
nothing to do with missingness in your data.
The error message is pretty clear: for some reason 'if (abs(x - oldx)
ftol)', which looks like a check for convergence, doesn't evaluate to
TRUE or FALSE as expected. Perhaps due to the warning message about
problems with NaN in the starting values? Have you checked your data?
That warning message is typical for when you try to take logs of a
negative number:
log(-1)
[1] NaN
Warning message:
In log(-1) : NaNs produced
Unless this helps you identify the problem, we need a (preferably small)
reproducible example demonstrating the issue to be able to provide
further help.
BTW, have you asked the package maintainer (as per the posting guide)?
Henric Winell
--
View this message in context:
http://r.789695.n4.nabble.com/Error-in-if-abs-x-oldx-ftol-when-using-lognormal-distribution-in-mixed-logit-tp4710284.html
Sent from the R help mailing list archive at Nabble.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-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] building a quicksort function in rcpp
Hi I am using RCPP to build a C++ function for quicksort called qsort.
This function is compiled and loaded through the cxxfunction in R
I am getting the message in R error: no matching function for call to
'qsort(int*)' The code is below.
It will not run for me and I was wondering if you could help?
library(Rcpp)
library(inline)
incl - 'int qsort(int xx[], int left, int right) {
int i = left,
j = right;
int tmp;
int pivot = xx[(left + right) / 2];
/* partition */
while (i = j) {
while (xx[i] pivot)
i++;
while (xx[j] pivot)
j--;
if (i = j) {
tmp = xx[i];
xx[i] = xx[j];
xx[j] = tmp;
i++;
j--;
}
}
/* recursion */
if (left j){
qsort(xx, left, j);
}
if (i right){
qsort(xx, i, right);
}
return (qsort(xx));
}
'
sortCpp - cxxfunction(signature( x = integer,left = integer,
right = integer),
body = 'IntegerVector arr(x);
int a = asint(left);
int b = asint(right);
return wrap(qsort(arr));',
include = incl,
plugin = Rcpp,
verbose = TRUE)
[[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] Infinite Series
Thanks Bert! On Fri, Jul 24, 2015 at 7:57 PM, Bert Gunter bgunter.4...@gmail.com wrote: Janh: It sounds like you really need to go through an R tutorial or two before posting further, as this is a pretty basic query. Or am I wrong about this? An answer: Just use indexing cumsum(1/seq_len(100)^2)[seq(10, to = 100,by = 10)] ## keeps every 10th [1] 1.549768 1.596163 1.612150 1.620244 1.625133 1.628406 1.630750 1.632512 1.633884 [10] 1.634984 But beware FAQ 7.31 for long series. Cheers, Bert Bert Gunter Data is not information. Information is not knowledge. And knowledge is certainly not wisdom. -- Clifford Stoll On Fri, Jul 24, 2015 at 4:37 PM, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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. [[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] Infinite Series
Wow! So many (simpler) ways to skin a cat. Thanks! On Fri, Jul 24, 2015 at 8:07 PM, David Winsemius dwinsem...@comcast.net wrote: On Jul 24, 2015, at 4:37 PM, Janh Anni wrote: Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Wouldn't that just mean using sum instead of cumsum? Can even check the error from the analytical limit. sum(1/(1:100)^2) - pi^2/6 [1] -0.009950167 Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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. David Winsemius Alameda, CA, USA [[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] [FORGED] Simulating multivariate gamma
On 25/07/15 07:59, gmoyeyemi wrote: Hi, I'm having problem simulating multivariate gamma. Is there anyone to assist in simulating multivariate gamma. I know that for multivariate normal, we can use; mvrnorm (n, means, sigma) For starters you have to specify exactly what you mean by multivariate gamma; there is not a *unique* multivariate gamma distribution. A little bit of googling on multivariate gamma will lead you to some useful material. In particular there is a reference to the copula package which apparently provides a means of simulating a multivariate distribution with gamma marginals. It is not however clear to me how one specifies the desired correlation structure, or what the limitations on such a structure are. I find the documentation to be opaque. Perhaps someone with knowledge and insight on this issue will chime in. cheers, Rolf Turner -- Technical Editor ANZJS Department of Statistics University of Auckland Phone: +64-9-373-7599 ext. 88276 __ 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] about R 3.2.0
Dear sir, I am using currently R 3.1.3. But i wnat to upgrade this version to R 3.2.0 but i am feared that the libraries which i have installed may be remove? please guide me. thanks -- Waqas Shafqat Chattha Ph. D Scholar Department of Plant Breeding and Genetics University of Agriculture, Faisalabad Pakistan [[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] Differences in output of lme() when introducing interactions
I clearly am going to have to improve my stats knowledge by reading McPhearson. To heck with Senn- too complicated. :) Thanks Terry. John Kane Kingston ON Canada -Original Message- From: thern...@mayo.edu Sent: Thu, 23 Jul 2015 14:07:00 -0500 To: r.tur...@auckland.ac.nz, thern...@mayo.edu Subject: Re: [R] Differences in output of lme() when introducing interactions The following are in parody (but like all good parody correct wrt the salient features). The musings of Guernsey McPhearson http://www.senns.demon.co.uk/wprose.html#Mixed http://www.senns.demon.co.uk/wprose.html#FDA In formal publication: Senn, Statistical Issues in Drug Development, second edition, Chapter 14: Multicentre Trials Senn, The many modes of meta, Drug information journal, 34:535-549, 2000. The second points out that in a meta analysis no one would ever consider giving both large and small trials equal weights, and relates that to several other bits of standard practice. The 'equal weights' notion embedded in a fixed effects model + SAS type 3 is an isolated backwater. Terry T. PS. The Devils' Drug Development Dictionary at the same source has some gems. Three rather random choices: Bayesian - One who, vaguely expecting a horse and catching a glimpse of a donkey, strongly concludes he has seen a mule. Medical Statistician - One who won't accept that Columbus discovered America because he said he was looking for India in the trial Plan. Trend Towards Significance - An ever present help in times of trouble. On 07/22/2015 06:02 PM, Rolf Turner wrote: On 23/07/15 01:15, Therneau, Terry M., Ph.D. wrote: SNIP 3. Should you ever use it [i.e. Type III SS]? No. There is a very strong inverse correlation between understand what it really is and recommend its use. Stephen Senn has written very intellgently on the issues. Terry --- can you please supply an explicit citation? Ta. cheers, Rolf __ 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 ONLINE PHOTOSHARING - Share your photos online with your friends and family! Visit http://www.inbox.com/photosharing to find out more! __ 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] Table Looks Funny
Hi Marrisa, As a follow-up to Jim's point, it might be a good idea to supply the data. Since you don't trust the imported data our preferred method of using dput() won't work but if you rename the csv file to whatever.txt and attached it should make it through. John Kane Kingston ON Canada -Original Message- From: marissa.fahlb...@gmail.com Sent: Thu, 23 Jul 2015 16:08:10 -0500 To: r-help@r-project.org Subject: [R] Table Looks Funny Hey, I can't seem to import my csv file in such a way that the table looks normal. The dimensions are correct, 4x7, and I set my header =TRUE, but it still looks weird. Attached is the picture. Any ideas?? Thanks!! -Marissa 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.
[R] apply kendall tau to a split data set
$`19179222` Unique.IDStart.YearL1.Risk.Category Gross.amount.sum 17 19179222 2013 Execution, Delivery Process Management 161212.1 18 19179222 2015 Execution, Delivery Process Management 110880.0 $`25182498` Unique.ID Start.YearL1.Risk.Category Gross.amount.sum 19 25182498 2014 Clients, Products Business Practices 59384 20 25182498 2014 Execution, Delivery Process Management 355000 21 25182498 2015 Execution, Delivery Process Management 27720 $`32506027` Unique.IDStart.YearL1.Risk.Category Gross.amount.sum 22 32506027 2003 Execution, Delivery Process Management 360.0 23 32506027 2013 Execution, Delivery Process Management 161212.1 24 32506027 2014 Clients, Products Business Practices 14846.0 Hi, I have split a data frame and output is as above. I would like to apply Kendall's tau to calculate correlations. For example, for the last Unique.ID 32506027, I want to create a time series for each L1 risk category, and then calculate the correlation between each L1 risk category using the Kendall tau approach. Any help would be much appreciated. Thanks s -- View this message in context: http://r.789695.n4.nabble.com/apply-kendall-tau-to-a-split-data-set-tp4710303.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Labeling world map
I draw world map using library(maptools) library(ggmap) library(mapdata) library(maps) map(world,fill=TRUE,col=White,bg=light blue,ylim=c(-60,90),mar=c(0,0,0,0)) native - c(brazil,sao paulo state) nat -geocode(native) nat.x - nat$lon nat.y - nat$lat points(nat.x,nat.y,col=yellow,pch=16) How can i put lilte for this map and label points -- View this message in context: http://r.789695.n4.nabble.com/Labeling-world-map-tp4710296.html Sent from the R help mailing list archive at Nabble.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] “Error in if (abs(x - oldx) ftol)” when using “lognormal” distribution in mixed logit
Hi Henric,
Thank you for your reply! It really helps. I should have noticed this
earlier. I don't have a negative input, the error is because our survey
allowed people to choose neither of the choices we gave, so we added a
choice Neither with both deductible and premium being 0, which caused
this problem. I tried to delete the 0 entries just now and it worked! I
think I need to find a way do deal with the Neither choice in another way.
Thank you so much and have a nice weekend!
Best, Dong
On Fri, Jul 24, 2015 at 7:16 AM, Henric Winell nilsson.hen...@gmail.com
wrote:
Den 2015-07-24 kl. 00:33, skrev Dera:
Hi, I have a question about how to use the mlogit package in R to do
analysis
of discrete choice survey data. Our survey is about asking people to
choose
from different insurance policies(with two attributes of deductible and
premium).
The code I used to fit mixed logit is:
[1] ml - mlogit.data (mydata, choice=choice, shape = wide, id =
individual,
opposite =c ('deductible', 'premium'),varying = 5:10)
[2] ml.w5 - mlogit (choice~deductible+premium|0, ml, panel = TRUE,
rpar = c(deductible='ln', premium='ln'),
R = 100, halton = NA, print.level=0)
I try to use lognormal because we hope the coefficients for both
deductible
and premium are negative. And I use opposite in [1] to reverse the sign
because lognormal is always positive.
But I always get the error warning:
Error in if (abs(x - oldx) ftol) { : missing value where TRUE/FALSE
needed
In addition: Warning message: In log(start[ln]) : NaNs produced
I double check the data and am sure there isn't any missing data. And if I
change the lognormal ln to n or cn, it will work without any
warning.
Does anyone know how to deal with this? Thank you for your help.
I've never used the 'mlogit' package but that error message has likely
nothing to do with missingness in your data.
The error message is pretty clear: for some reason 'if (abs(x - oldx)
ftol)', which looks like a check for convergence, doesn't evaluate to TRUE
or FALSE as expected. Perhaps due to the warning message about problems
with NaN in the starting values? Have you checked your data? That warning
message is typical for when you try to take logs of a negative number:
log(-1)
[1] NaN
Warning message:
In log(-1) : NaNs produced
Unless this helps you identify the problem, we need a (preferably small)
reproducible example demonstrating the issue to be able to provide further
help.
BTW, have you asked the package maintainer (as per the posting guide)?
Henric Winell
--
View this message in context:
http://r.789695.n4.nabble.com/Error-in-if-abs-x-oldx-ftol-when-using-lognormal-distribution-in-mixed-logit-tp4710284.html
Sent from the R help mailing list archive at Nabble.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.
[R] interactive Map with option to slide through years
Hello,
first of all: my english is horrible but I try to explain what I want to
say.
I am new to R and thank to your help I managed to create an interactive map
of Germany for some weather data. I used
States = data.frame(Datensatz)
require(googleVis)
G4 = gvisGeoChart(States,
locationvar = ISO,
colorvar = Hoechsttemperatur, hovervar = name,
options=list(
width=800, height=600, region=DE,
displayMode=regions,
resolution=provinces, colorAxis={colors:
['yellow','red']}))
plot(G4)
plot(G4, 'chart')
for the map. Now I would like to create a map that shows the data for
different years. I would like to do something like this:
http://r.789695.n4.nabble.com/file/n4710322/Bildschirmfoto_2015-07-24_um_23.png
Is there an easy possibility (I am really really new to R) to do so? Again,
I am very sorry for my bad english.
Thank you very very much,
Marie-Louise
--
View this message in context:
http://r.789695.n4.nabble.com/interactive-Map-with-option-to-slide-through-years-tp4710322.html
Sent from the R help mailing list archive at Nabble.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] Infinite Series
cumsum(1/(1:100)^2)[100] On Jul 24, 2015, at 4:37 PM, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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-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] Infinite Series
On Jul 24, 2015, at 4:37 PM, Janh Anni wrote: Hello Jeff, Thanks a lot. I tried it and see that it prints out the entire 100 partial sums, so I can take the last value as the partial sum for the first 100 terms. Would there be any way cumsum can print only the nth partial sum, i.e. the last value in the array, instead of printing the entire array? Thanks again. Wouldn't that just mean using sum instead of cumsum? Can even check the error from the analytical limit. sum(1/(1:100)^2) - pi^2/6 [1] -0.009950167 Joseph On Fri, Jul 24, 2015 at 2:02 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: Please reply-all so the mailing list stays in the loop. cumsum(1/(1:100)^2) gives you the partial sums up through i=100. --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 24, 2015 10:30:09 AM PDT, Janh Anni annij...@gmail.com wrote: Hello Jeff, Thank you so much for the suggestion, I searched cumsum as suggested but not sure it is what I had in mind. For instance if I had the infinite series:[image: Inline image 1] and want to compute the sum of the, say, first 100 terms, how could I use cusum to do that? Thanks again, Janh On Thu, Jul 23, 2015 at 11:51 PM, Jeff Newmiller jdnew...@dcn.davis.ca.us wrote: ?cumsum --- Jeff NewmillerThe . . Go Live... DCN:jdnew...@dcn.davis.ca.usBasics: ##.#. ##.#. Live Go... Live: OO#.. Dead: OO#.. Playing Research Engineer (Solar/BatteriesO.O#. #.O#. with /Software/Embedded Controllers) .OO#. .OO#. rocks...1k --- Sent from my phone. Please excuse my brevity. On July 23, 2015 8:23:39 PM PDT, Janh Anni annij...@gmail.com wrote: Dear All, Does anyone know of any R functions that compute partial sums of series? Thanks in advance! Janh [[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. David Winsemius Alameda, CA, USA __ 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] P value from jaccard's index matrix
My table having 40 raw and 4 columns, in that 4 columns first column belongs to one group and the remaining constitute the other group. using following commands for calculating jaccard's index x - read.csv(file name,header=T, sep= ) jac - vegdist(x,method=jaccard) from this out file(jac) how can i find the p value for two groups ? and how can i plot notched box plot of these two groups? when i use boxes (as.matrix(jac)~x$first column,notch=TRUE) it showing 40 box plots.why it so? -- View this message in context: http://r.789695.n4.nabble.com/P-value-from-jaccard-s-index-matrix-tp4710302.html Sent from the R help mailing list archive at Nabble.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] interactive Map: Popups
You guys are awesome thank you all very very much! -- View this message in context: http://r.789695.n4.nabble.com/interactive-Map-Popups-tp4710226p4710295.html Sent from the R help mailing list archive at Nabble.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] How to calculate the average direct effect, average total effect and average indirect effect for spatial regression models with spatial lag of dependent variable
Dear Linus Holtermann, thank a lot for telling me the key to calculate the effects. I will try it. thank you for your help! best regards, Wenyue Yang -- View this message in context: http://r.789695.n4.nabble.com/How-to-calculate-the-average-direct-effect-average-total-effect-and-average-indirect-effect-for-spate-tp4710253p4710315.html Sent from the R help mailing list archive at Nabble.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] Simulating multivariate gamma
Hi, I'm having problem simulating multivariate gamma. Is there anyone to assist in simulating multivariate gamma. I know that for multivariate normal, we can use; mvrnorm (n, means, sigma) Thanks. __ 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.
