[R] Paths in knitr

[Yihui Xie]

Will there be anything wrong if you do not set these options?

Regards,
Yihui
--
https://yihui.name


On Mon, Jun 12, 2017 at 2:24 AM,  <G.Maubach at weinwolf.de> wrote:
> Hi Yihui,
> Hi Duncan,
>
> I corrected my typo. Unfortunately knitr did not find my plots in the
> directory where they reside which is different from the Rmd document.
>
> The documentation of knitr says:
>
> base.dir: (NULL) an absolute directory under which the plots are generate
> root.dir: (NULL) the root directory when evaluating code chunks; if NULL,
> the directory of the input document will be used
>
> From that description I thought, if the base.dir can be used for writng
> plots, it is then also used for reading plots if set? No, it is not.
> If I set the root directory to the plots/graphics directory will knitr
> then find my plots? No, it does not.
>
> Reading blog posts my thoughts looked not so strange to me, e.g.
> https://philmikejones.wordpress.com/2015/05/20/set-root-directory-knitr/.
> Unfortunately, it does not work for me.
>
> I am using a RStudio project file. Could it be that this interferes which
> the knitr options?
>
> I tried the solution that Duncan suggested:
>
> c_path_plots <-
> "H:/2017/Analysen/Kundenzufriedenheit/Auswertung/results/graphics
>
> `r knitr::include_graphics(file.path(c_path_plots,
> "email_distribution_pie.png"))`
>
> This solution works fine. I will go with it for this project as I have to
> finish my report soon.
>
> I read Hadley's book on bulding R Packages (
> https://www.amazon.de/R-Packages-Hadley-Wickham/dp/1491910593) and found
> it quite complicated and time consuming to build one. Thus I did not try
> yet to build my own packages. At the end of last week I heard from another
> library (http://reaktanz.de/R/pckg/roxyPackage/) which shall make building
> packages much easier. I plan to try that shortly.
>
> On my path to become better in analytics using R, I will try to use
> modules of Rmd files which can then easily be integrated into a Rmd
> report. I have yet to see how I can include these file into a complete
> report.
>
> Kind regards
>
> Georg
>
>
> ----- Weitergeleitet von Georg Maubach/WWBO/WW/HAW am 12.06.2017 08:47
> -----
>
> Von:    Yihui Xie <xie at yihui.name>
> An:     G.Maubach at gmx.de,
> Kopie:  R Help <r-help at r-project.org>
> Datum:  09.06.2017 20:53
> Betreff:        Re: [R] Paths in knitr
> Gesendet von:   "R-help" <r-help-bounces at r-project.org>
>
>
>
> I'd say it is an expert-only option. If you do not understand what it
> means, I strongly recommend you not to set it.
>
> Similarly, you set the root_dir option and I don't know why you did it,
> but
> it is a typo anyway (should be root.dir).
>
> Regards,
> Yihui
> --
> https://yihui.name
>
> On Fri, Jun 9, 2017 at 4:50 AM, <G.Maubach at gmx.de> wrote:
>
>> Hi Yi,
>>
>> many thanks for your reply.
>>
>> Why I do have to se the base.dir option? Cause, to me it is not clear
> from
>> the documentation, where knitr looks for data files and how I can adjust
>> knitr to tell it where to look. base.dir was a try, but did not work.
>>
>> Can you give me a hint where I can find information/documentation on
> this
>> path issue?
>>
>> Kind regards
>>
>> Georg
>>
>>
>> > Gesendet: Donnerstag, 08. Juni 2017 um 15:05 Uhr
>> > Von: "Yihui Xie" <xie at yihui.name>
>> > An: G.Maubach at weinwolf.de
>> > Cc: "R Help" <r-help at r-project.org>
>> > Betreff: Re: [R] Paths in knitr
>> >
>> > Why do you have to set the base.dir option?
>> >
>> > Regards,
>> > Yihui
>> > --
>> > https://yihui.name
>> >
>> >
>> > On Thu, Jun 8, 2017 at 6:15 AM,  <G.Maubach at weinwolf.de> wrote:
>> > > Hi All,
>> > >
>> > > I have to compile a report for the management and decided to use
>> RMarkdown
>> > > and knitr. I compiled all needed plots (using separate R scripts)
>> before
>> > > compiling the report, thus all plots reside in my graphics
> directory.
>> The
>> > > RMarkdown report needs to access these files. I have defined
>> > >
>> > > ```{r setup, include = FALSE}
>> > > knitr::opts_knit$set(
>> > >   echo = FALSE,
>> > >   xtable.type = "html",
>> > >   base.dir = "H:/2017/Analysen/Kundenzufriedenheit/Auswertung",
>> > >   root_dir = "H:/2017/Analysen/Kundenzufriedenheit/Auswertung",
>> > >   fig.path = "results/graphics")  # relative path required, see
>> > > http://yihui.name/knitr/options
>> > > ```
>> > >
>> > > and then referenced my plot using
>> > >
>> > > <img src = "email_distribution_pie.png"></img>
>> > >
>> > > because I want to be able to customize the plotting attributes.
>> > >
>> > > But that fails with the message "pandoc.exe: Could not fetch
>> > > email_distribution_pie.png".
>> > >
>> > > If I give it the absolute path
>> > > "H:/2017/Analysen/Kundenzufriedenheit/Auswertung/results/
>> graphics/email_distribution_pie.png"
>> > > it works fine as well if I copy the plot into the directory where
> the
>> > > report.RMD file resides.
>> > >
>> > > How can I tell knitr to fetch the ready-made plots from the graphics
>> > > directory?
>> > >
>> > > Kind regards
>> > >
>> > > Georg
>>
>
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