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James Jong

2013-Feb-07 18:36 UTC

[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

	[[alternative HTML version deleted]]

John Kane

2013-Feb-07 18:57 UTC

head link

[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: ribonucleico at gmail.com
> Sent: Thu, 7 Feb 2013 13:36:56 -0500
> To: r-help at 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
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at 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.
____________________________________________________________
FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop!

Nordlund, Dan (DSHS/RDA)

2013-Feb-07 20:09 UTC

head link

[R] Sourcing my file does not print command outputs

> -----Original Message-----
> From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-
> project.org] On Behalf Of John Kane
> Sent: Thursday, February 07, 2013 10:57 AM
> To: James Jong; r-help at 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: ribonucleico at gmail.com
> > Sent: Thu, 7 Feb 2013 13:36:56 -0500
> > To: r-help at 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

James Jong

2013-Feb-07 21:48 UTC

head link

[R] Fwd: 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) <
NordlDJ@dshs.wa.gov> wrote:
> I don’t know where resamps  comes from and I don’t know what parameters
> you provided to source(), so you haven’t 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:ribonucleico@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) <
> NordlDJ@dshs.wa.gov<mailto:NordlDJ@dshs.wa.gov>> wrote:
> > -----Original Message-----
> > From:
r-help-bounces@r-project.org<mailto:r-help-bounces@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: ribonucleico@gmail.com<mailto:ribonucleico@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]]

James Jong

2013-Feb-07 22:10 UTC

head link

[R] Sourcing my file does not print command outputs

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) <
NordlDJ@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:ribonucleico@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) <
> NordlDJ@dshs.wa.gov> wrote:****
>
> I don’t know where resamps  comes from and I don’t know what parameters
> you provided to source(), so you haven’t 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:ribonucleico@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) <
> NordlDJ@dshs.wa.gov<mailto:NordlDJ@dshs.wa.gov>> wrote:
> > -----Original Message-----****
>
> > From:
r-help-bounces@r-project.org<mailto:r-help-bounces@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: ribonucleico@gmail.com<mailto:ribonucleico@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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