[R] Debugging Rmarkdown

[Patrick Connolly]

knitr::purl -- thats a great tip!  As soon as got hold of a reqular .R
script, I spotted the reason why my Fmd file wouldn't knit in a matter
of seconds.  Thank you Jeff.  Thanks also to all the other suggestions.



On Fri, 19-Apr-2019 at 02:44PM -0700, Jeff Newmiller wrote:

|> I just run each chunk in sequence starting from an fresh restart of
|> R by copying code to the R console. However you can use knitr::purl
|> to extract all of the code into a regular R script to do whatever
|> debugging you are most familiar with.


|> On April 19, 2019 2:03:00 PM PDT, Patrick Connolly <p_connolly using slingshot.co.nz> wrote:
|> >
|> >On 19/04/19 12:13 AM, Thierry Onkelinx wrote:
|> >> Dear Patrick,
|> >>
|> >> This is not easy to debug without a reprex
|> >>
|> >> I would check the content of zzz and wide.i in the loop
|> >>
|> >> str(wide.i)
|> >>  zzz <- rbind(zzz, wide.i)
|> >> str(zzz)
|> >>
|> >That's just what I'm trying to achieve but the debugging doesn't work 
|> >how it does with regular R code.
|> >
|> >> Note that the Rmd always runs in a clean environment. This might 
|> >> explain the difference
|> >>
|> >The data frames xx and yy are defined in earlier code chunks. Maybe I 
|> >need to define them again.
|> >
|> >
|> >I'll look closer at it after Easter.
|> >
|> >
|> >Thanks for the suggestion.
|> >
|> >> Best regards,
|> >>
|> >> ir. Thierry Onkelinx
|> >> Statisticus / Statistician
|> >>
|> >> Vlaamse Overheid / Government of Flanders
|> >> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR
|> >NATURE 
|> >> AND FOREST
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|> >> thierry.onkelinx using inbo.be <mailto:thierry.onkelinx using inbo.be>
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|> >>
|> >>
|> >///////////////////////////////////////////////////////////////////////////////////////////
|> >> To call in the statistician after the experiment is done may be no 
|> >> more than asking him to perform a post-mortem examination: he may be 
|> >> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
|> >> The plural of anecdote is not data. ~ Roger Brinner
|> >> The combination of some data and an aching desire for an answer does 
|> >> not ensure that a reasonable answer can be extracted from a given
|> >body 
|> >> of data. ~ John Tukey
|> >>
|> >///////////////////////////////////////////////////////////////////////////////////////////
|> >>
|> >> <https://www.inbo.be>
|> >>
|> >>
|> >> Op do 18 apr. 2019 om 11:53 schreef Patrick Connolly 
|> >> <p_connolly using slingshot.co.nz <mailto:p_connolly using slingshot.co.nz>>:
|> >>
|> >>     I have a function that works in ESS, but it fails if I include it
|> >in
|> >>     an .Rmd file that I tried to knit using Rstudio.  I found advice
|> >at:
|> >>    
|> >https://www.rstudio.com/products/rstudio/release-notes/debugging-with-rstudio/
|> >>
|> >>     It seems to be not referring to markdown files.  Somewhere else
|> >>     suggested calling render() in the console pane.  I tried that. 
|> >The
|> >>     browser() function interrupts correctly, but I can't find out
|> >what the
|> >>     object zzz in the code below looks like.  Nothing prints the way
|> >it
|> >>     would in a "normal" R buffer.
|> >>
|> >>     code outline:  making zzz out of two dataframes xx and yy
|> >>
|> >>     ##
|> >>         zzz <- NULL
|> >>         for(i in xx$Sample){
|> >>             raw.i <- <stuff>
|> >>
|> >>             etc. etc.
|> >>
|> >>             zzz <- rbind(zzz, wide.i)
|> >>     }
|> >>        browser()
|> >>
|> >>         names(zzz) <- c("Cultivar", "Test", "Change")
|> >>     That line fails, with a complaint about zzz being NULL.
|> >>
|> >>     It appears as though the rbind doesn't do anything, but I can't
|> >see
|> >>     what wide.i looks like to get an idea what could be the cause.
|> >>
|> >>     Ideas what I should try are welcome.  I have no idea why the code
|> >>     works in an R environment but not an Rmd one.
|> >>
|> >>
|> >>     R-3.5.2,
|> >>     platform       x86_64-pc-linux-gnu
|> >>     arch           x86_64
|> >>     os             linux-gnu
|> >>     system         x86_64, linux-gnu
|> >>
|> >>     Rstudio Version 1.1.383
|> >>
|> >>
|> >>
|> >>     -- 
|> >>    
|> >~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >>
|> >>        ___    Patrick Connolly
|> >>      {~._.~}                   Great minds discuss ideas
|> >>      _( Y )_                 Average minds discuss events
|> >>     (:_~*~_:)                  Small minds discuss people
|> >>      (_)-(_)                              ..... Eleanor Roosevelt
|> >>
|> >>    
|> >~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.
|> >>
|> >>     ______________________________________________
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|> >>     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 using 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.
|> 
|> -- 
|> Sent from my phone. Please excuse my brevity.

-- 
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.   
   ___    Patrick Connolly   
 {~._.~}                   Great minds discuss ideas    
 _( Y )_  	         Average minds discuss events 
(:_~*~_:)                  Small minds discuss people  
 (_)-(_)  	                      ..... Eleanor Roosevelt
	  
~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.