Thanks Dan. The ... is an accidental typo in the email. Would you mind verifying that dotplot opens a plot *without* print.eval=TRUE?
Thanks, J. On Thu, Feb 7, 2013 at 5:08 PM, Nordlund, Dan (DSHS/RDA) < nord...@dshs.wa.gov> wrote: > James,**** > > ** ** > > Your code seems to have sitting on a line all by itself (maybe should > be at the end of the preceding comment? Anyway, when I eliminated that > problem and sourced the script using the following call**** > > ** ** > > source(c:/tmp/test_source.R, print.eval=TRUE)**** > > ** ** > > The summary information and dotplot printed just fine.**** > > ** ** > > Dan**** > > ** ** > > Daniel J. Nordlund**** > > Washington State Department of Social and Health Services**** > > Planning, Performance, and Accountability**** > > Research and Data Analysis Division**** > > Olympia, WA 98504-5204**** > > ** ** > > *From:* James Jong [mailto:ribonucle...@gmail.com] > *Sent:* Thursday, February 07, 2013 1:48 PM > *To:* Nordlund, Dan (DSHS/RDA) > > *Subject:* Re: [R] Sourcing my file does not print command outputs**** > > ** ** > > Thanks Dan,**** > > ** ** > > Here is a minimal full example, where dotplot fails to print anything if I > source the file. I have tried restarting R and directly sourcing this file > without doing anything else first (my .Rprofile is empty). This is running > on Linux with the latest stable version of R.**** > > ** ** > > ========================================**** > > #Setup**** > > rm(list = ls(all = TRUE))**** > > set.seed(1)**** > > ** ** > > #Generate an input matrix with 10,000 values**** > > #2,000 rows, 5 columns**** > > X <- data.frame(replicate(5, rnorm(2000)))**** > > ** ** > > #Construct Y using X**** > > Y <- runif(1)*X[,1]*X[,2]^2+runif(1)*X[,3]/X[,4]**** > > ** ** > > #Convert Y to binary**** > > Y <- as.factor(ifelse(sign(Y)>0,'X1','X0'))**** > > ** ** > > #Create bootstrap samples for fitting models**** > > library(caret)**** > > print("Creating bootstrap samples")**** > > tmp <- createResample(Y,times = 25)**** > > myCtrl <- trainControl(method = "boot", index = tmp, timingSamps = 10)**** > > ** ** > > ** ** > > RFmodel <- train(X,Y,method='rf',trControl=myCtrl,tuneLength=1) *** > * > > ** ** > > NNmodel <- train(X,Y,method='nnet',trControl=myCtrl,tuneLength=3, trace = > FALSE)**** > > ## GLMnet = GLMmodel,**** > > ** ** > > ... **** > > ** ** > > #Assess re-sampled (out of sample) accuracy**** > > print("Assessing re-sampled (OOB) accuracy")**** > > resamps <- resamples(**** > > list( RF = RFmodel,**** > > NN = NNmodel**** > > ))**** > > print("Summarizing resamps")**** > > summary(resamps)**** > > ** ** > > dotplot(resamps, metric = "Accuracy")**** > > ========================================**** > > ** ** > > Thanks,**** > > ** ** > > James**** > > ** ** > > On Thu, Feb 7, 2013 at 4:37 PM, Nordlund, Dan (DSHS/RDA) < > nord...@dshs.wa.gov> wrote:**** > > I dont know where resamps comes from and I dont know what parameters > you provided to source(), so you havent provided a reproducible example. > But, did you call source with print.eval=TRUE ?**** > > > Dan > > Daniel J. Nordlund > Washington State Department of Social and Health Services > Planning, Performance, and Accountability > Research and Data Analysis Division > Olympia, WA 98504-5204**** > > From: James Jong [mailto:ribonucle...@gmail.com] > Sent: Thursday, February 07, 2013 1:30 PM > To: Nordlund, Dan (DSHS/RDA) > Cc: r-help@r-project.org**** > > Subject: Re: [R] Sourcing my file does not print command outputs**** > > Thanks. Interestingly I am having the same problem with > dotplot(resamps, metric = "Accuracy") > > Nothing shows up if I source the file. But I can visualize it I call this > command from the command line... Any thoughts? > > Thanks again, > > James**** > > On Thu, Feb 7, 2013 at 3:09 PM, Nordlund, Dan (DSHS/RDA) < > nord...@dshs.wa.gov<mailto:nord...@dshs.wa.gov>> wrote: > > -----Original Message-----**** > > > From: r-help-boun...@r-project.org<mailto:r-help-boun...@r-project.org> > [mailto:r-help-bounces@r-<mailto:r-help-bounces@r-> > > project.org<http://project.org>] On Behalf Of John Kane > > Sent: Thursday, February 07, 2013 10:57 AM**** > > > To: James Jong; r-help@r-project.org<mailto:r-help@r-project.org> > > Subject: Re: [R] Sourcing my file does not print command outputs > > > > From ?source > > "Note that running code via source differs in a few respects from > > entering it at the R command line. Since expressions are not executed > > at the top level, auto-printing is not done. So you will need to > > include explicit print calls for things you want to be printed" > > > > John Kane > > Kingston ON Canada > > > > > > > -----Original Message-----**** > > > > From: ribonucle...@gmail.com<mailto:ribonucle...@gmail.com> > > > Sent: Thu, 7 Feb 2013 13:36:56 -0500**** > > > > To: r-help@r-project.org<mailto:r-help@r-project.org> > > > Subject: [R] Sourcing my file does not print command outputs > > > > > > I looked at the documentation of source() and summary(), and I could > > not > > > find the reason why calling something like: > > > > > >> summary(resamps) > > > > > > from the command line, works (it prints the summary) > > > > > > whereas calling > > > > > > summary(resampls) > > > > > > from a file that I source with source("my_file.r") does not print > > > anything. > > > > > > How can I get summary(resamps) to print when I source a file with > > this > > > command? > > > > > > Thanks, > > > > > > James > > > > James, > > You might also want to look at ?source for the echo or print.eval > parameters to the source() function. Using > > source("my_file.r", echo=TRUE) > > or > > source("my_file.r", print.eval=TRUE) > > may get you what you want without adding explicit print statements to your > script file. > > > Hope this is helpful, > > Dan > > Daniel J. Nordlund > Washington State Department of Social and Health Services > Planning, Performance, and Accountability > Research and Data Analysis Division > Olympia, WA 98504-5204 > > > ______________________________________________**** > > R-help@r-project.org<mailto:R-help@r-project.org> mailing list**** > > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > **** > > [[alternative HTML version deleted]] > > > ______________________________________________ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.**** > > ** ** > [[alternative HTML version deleted]]
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