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John Sorkin

2009-Dec-31 14:29 UTC

[R] Obtaining partial output from a function that does not run to completion.

I have written a function that contains runs 
lm()
vif()  and
glm()

When the glm() blows up with an error message, I don't get the output from
either the lm() or vf() even thought neither lm() nor vif() have any problems .
How can I force the function to print sequential results rather than wait for
the entire function to complete before listing the functhion's output?
Thanks,
John



minBMI<-function(SS,SimData)
{
SampleData<-sample(1:SS,size=SS,replace=TRUE)
fitBMIEpiRevlm<-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
print(summary(fitBMIEpiRevlm))
print(vif(fitBMIEpiRevlm))
fitBMIEpiRev<-
glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(link="log"))

print(summary(fitBMIEpiRev))
}
minBMI(SS,SimData)  


John David Sorkin M.D., Ph.D.
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to faxing)

Confidentiality Statement:
This email message, including any attachments, is for th...{{dropped:6}}

Duncan Murdoch

2009-Dec-31 15:19 UTC

head link

[R] Obtaining partial output from a function that does not run to completion.

On 31/12/2009 9:29 AM, John Sorkin wrote:> I have written a function that contains runs 
> lm()
> vif()  and
> glm()
> 
> When the glm() blows up with an error message, I don't get the output
from either the lm() or vf() even thought neither lm() nor vif() have any
problems . How can I force the function to print sequential results rather than
wait for the entire function to complete before listing the functhion's
output?
Call print, e.g.

print(x <- lm(...))
print(y <- vif(...))
etc.

Duncan Murdoch
> Thanks,
> John
> 
> 
> 
> minBMI<-function(SS,SimData)
> {
> SampleData<-sample(1:SS,size=SS,replace=TRUE)
>
fitBMIEpiRevlm<-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
> print(summary(fitBMIEpiRevlm))
> print(vif(fitBMIEpiRevlm))
> fitBMIEpiRev<-
glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(link="log"))
> 
> print(summary(fitBMIEpiRev))
> }
> minBMI(SS,SimData)  
> 
> 
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> Confidentiality Statement:
> This email message, including any attachments, is for th...{{dropped:6}}
> 
> ______________________________________________
> 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.

David Winsemius

2009-Dec-31 15:21 UTC

head link

[R] Obtaining partial output from a function that does not run to completion.

On Dec 31, 2009, at 8:29 AM, John Sorkin wrote:
> I have written a function that contains runs
> lm()
> vif()  and
> glm()
>
> When the glm() blows up with an error message, I don't get the  
> output from either the lm() or vf() even thought neither lm() nor  
> vif() have any problems . How can I force the function to print  
> sequential results rather than wait for the entire function to  
> complete before listing the functhion's output?
> Thanks,
> John
I thought the usual method for graceful error recovery was to use the  
try or tryCatch functions.>
>minBMI<-function(SS,SimData)
{
SampleData<-sample(1:SS,size=SS,replace=TRUE)
fitBMIEpiRevlm<-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI  
+jMEDICAID+H_AGE+jMARSTAT +factor(jEDUCATION) +factor(jsmokercat) 
+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
print(summary(fitBMIEpiRevlm))
print(vif(fitBMIEpiRevlm))
#Perhaps (untested):
try( {
fitBMIEpiRev<- glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI 
+jMEDICAID+H_AGE +jMARSTAT+factor(jEDUCATION) +factor(jsmokercat) 
+factor(jrace)+log(INCOME_C 
+1),data=SimData[SampleData,],family=Gamma(link="log"))

print(summary(fitBMIEpiRev))
       } )
}
minBMI(SS,SimData)

-- 
David.

> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics

William Dunlap

2009-Dec-31 17:34 UTC

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[R] Obtaining partial output from a function that does not run to completion.

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of John Sorkin
> Sent: Thursday, December 31, 2009 6:30 AM
> To: r-help at r-project.org
> Subject: [R] Obtaining partial output from a function that 
> does not run to completion.
> 
> I have written a function that contains runs 
> lm()
> vif()  and
> glm()
> 
> When the glm() blows up with an error message, I don't get 
> the output from either the lm() or vf() even thought neither 
> lm() nor vif() have any problems . How can I force the 
> function to print sequential results rather than wait for the 
> entire function to complete before listing the functhion's output?
> Thanks,
> John
If you are using the Windows GUI version of R you may
be running into "output buffering", in which output is
not printed until the top level expression is done or
until enough output is generated.  The Misc\Buffered Output
menu item or pressing control-W will toggle output buffering.
If that fixes your problem, I think you can use dialog box
under the Edit\GUI Preferences ... menu item to set the
default value for output buffering.

Bill Dunlap
Spotfire, TIBCO Software
wdunlap tibco.com  
> 
> 
> 
> minBMI<-function(SS,SimData)
> {
> SampleData<-sample(1:SS,size=SS,replace=TRUE)
> fitBMIEpiRevlm<-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokerc>
at)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)> print(summary(fitBMIEpiRevlm))
> print(vif(fitBMIEpiRevlm))
> fitBMIEpiRev<- 
> glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+
> H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jr
> ace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(li
nk="log"))> 
> print(summary(fitBMIEpiRev))
> }
> minBMI(SS,SimData)  
> 
> 
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
> 
> Confidentiality Statement:
> This email message, including any attachments, is for 
> th...{{dropped:6}}
> 
> ______________________________________________
> 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.
>

Eric

2009-Dec-31 19:31 UTC

head link

[R] Obtaining partial output from a function that does not run to completion.

To heck with print(), use R's debugging capabilities instead:

trace ( minBMI, browser )

Be sure to ?trace and ?browser so you can figure out how to 
interactively debug.

Eric


On 12/31/09 6:29 AM, John Sorkin wrote:> I have written a function that contains runs
> lm()
> vif()  and
> glm()
>
> When the glm() blows up with an error message, I don't get the output
from either the lm() or vf() even thought neither lm() nor vif() have any
problems . How can I force the function to print sequential results rather than
wait for the entire function to complete before listing the functhion's
output?
> Thanks,
> John
>
>
>
> minBMI<-function(SS,SimData)
> {
> SampleData<-sample(1:SS,size=SS,replace=TRUE)
>
fitBMIEpiRevlm<-lm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],x=TRUE)
> print(summary(fitBMIEpiRevlm))
> print(vif(fitBMIEpiRevlm))
> fitBMIEpiRev<-
glm(AAMTCARE~BMIEpiRevAdjc+BMIEpiRevAdjcSq+SEX+jPHI+jMEDICAID+H_AGE+jMARSTAT+factor(jEDUCATION)+factor(jsmokercat)+factor(jrace)+log(INCOME_C+1),data=SimData[SampleData,],family=Gamma(link="log"))
>
> print(summary(fitBMIEpiRev))
> }
> minBMI(SS,SimData)
>
>
> John David Sorkin M.D., Ph.D.
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to faxing)
>
> Confidentiality Statement:
> This email message, including any attachments, is for th...{{dropped:6}}
>
> ______________________________________________
> 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.
>

R help - Dec 2009 - Obtaining partial output from a function that does not run to completion.

[R] Obtaining partial output from a function that does not run to completion.

[R] Obtaining partial output from a function that does not run to completion.

[R] Obtaining partial output from a function that does not run to completion.

[R] Obtaining partial output from a function that does not run to completion.

[R] Obtaining partial output from a function that does not run to completion.

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