[R] Debugging Rmarkdown

[Jeff Newmiller]

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
>> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
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>> Havenlaan 88 bus 73, 1000 Brussel
>> www.inbo.be <http://www.inbo.be>
>>
>>
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>> able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
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>> not ensure that a reasonable answer can be extracted from a given
>body 
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>>
>> <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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>>
>
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>
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