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) <
[email protected]> 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:[email protected]]
> Sent: Thursday, February 07, 2013 1:30 PM
> To: Nordlund, Dan (DSHS/RDA)
> Cc: [email protected]
> 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) <
> [email protected]<mailto:[email protected]>> wrote:
> > -----Original Message-----
> > From: [email protected]<mailto:[email protected]>
> [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; [email protected]<mailto:[email protected]>
> > 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: [email protected]<mailto:[email protected]>
> > > Sent: Thu, 7 Feb 2013 13:36:56 -0500
> > > To: [email protected]<mailto:[email protected]>
> > > 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
>
>
> ______________________________________________
> [email protected]<mailto:[email protected]> 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]]
>
>
> ______________________________________________
>
> [email protected] 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]]
______________________________________________
[email protected] 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.
