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_conno...@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 |> >> thierry.onkel...@inbo.be <mailto:thierry.onkel...@inbo.be> |> >> Havenlaan 88 bus 73, 1000 Brussel |> >> www.inbo.be <http://www.inbo.be> |> >> |> >> |> >/////////////////////////////////////////////////////////////////////////////////////////// |> >> 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_conno...@slingshot.co.nz <mailto:p_conno...@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 |> >> |> >> |> >~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. |> >> |> >> ______________________________________________ |> >> R-help@r-project.org <mailto:R-help@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. |> >> |> > |> > [[alternative HTML version deleted]] |> > |> >______________________________________________ |> >R-help@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 ~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~.~. ______________________________________________ R-help@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.
