[R] project path in Rmd

[Jeff Newmiller]

Where did this false dichotomy come from? The rmarkdown::render function has quite flexible parameters for compiling rmarkdown files in subdirectories without changing the current directory. And RStudio has a Global configuration to enable compiling using the Project directory as "current" under the RMarkdown settings.

On April 2, 2020 1:59:03 AM PDT, Ivan Calandra <calandra using rgzm.de> wrote:
>So what you're saying is that I should have scripts in the project
>directory and not in a subfolder within it, right?
>
>But what if I need (or at least want) to?
>
>Ivan
>
>--
>Dr. Ivan Calandra
>TraCEr, laboratory for Traceology and Controlled Experiments
>MONREPOS Archaeological Research Centre and
>Museum for Human Behavioural Evolution
>Schloss Monrepos
>56567 Neuwied, Germany
>+49 (0) 2631 9772-243
>https://www.researchgate.net/profile/Ivan_Calandra
>
>On 02/04/2020 10:56, Jeff Newmiller wrote:
>> Make it so. Outside R.
>>
>> At the command line, use cd before you start R. This should feel
>natural.
>>
>> In a GUI file browser, double clicking on a file type assigned to a
>program by default sets the containing directory to be current
>directory before kicking off the program, so double-clicking on an
>empty Project.RData file will do it. Or you can use RStudio
>Project.Rproj files the same way.
>>
>> On April 2, 2020 1:40:07 AM PDT, Ivan Calandra <calandra using rgzm.de>
>wrote:
>>> Hi Jeff,
>>>
>>> But if I do not use setwd(), the current working directory is NOT
>the
>>> project directory.
>>>
>>> That's what my problem is about... I guess I was not clear in my
>>> email...
>>>
>>> Ivan
>>>
>>> --
>>> Dr. Ivan Calandra
>>> TraCEr, laboratory for Traceology and Controlled Experiments
>>> MONREPOS Archaeological Research Centre and
>>> Museum for Human Behavioural Evolution
>>> Schloss Monrepos
>>> 56567 Neuwied, Germany
>>> +49 (0) 2631 9772-243
>>> https://www.researchgate.net/profile/Ivan_Calandra
>>>
>>> On 02/04/2020 10:37, Jeff Newmiller wrote:
>>>> I recommend not using setwd. Then you can always assume your
>current
>>> working directory is your project directory and reference relative
>to
>>> that.
>>>> On April 2, 2020 1:30:29 AM PDT, Ivan Calandra <calandra using rgzm.de>
>>> wrote:
>>>>> Dear useRs,
>>>>>
>>>>> I believe this is R code so appropriate for this list, but let me
>>> know
>>>>> if this relates more to RStudio itself.
>>>>>
>>>>> I am working on an RStudio project. In that project directory, I
>>> have a
>>>>> folder called 'analysis' and in there a folder called 'scripts'
>>>>> ('~/analysis/scripts').
>>>>> My data files needed for the scripts are in '~/analysis/raw_data'
>>> and
>>>>> the output should be in '~/analysis/derived_data'.
>>>>>
>>>>> My scripts are Rmd files, so when I knit them, their working
>>> directory
>>>>> is where they are located, i.e. '~/analysis/scripts'. The problem
>I
>>>>> then
>>>>> have is to specify the path for 'raw_data' and 'derived_data'
>since
>>>>> during the rendering I am not relative to the project directory
>>>>> anymore.
>>>>> And these folders are not subfolders of the working directory 
>>>>> '~/analysis/scripts'.
>>>>> I hope I am clear here...
>>>>>
>>>>> I would like to avoid absolute paths of course, but I do not know
>>> how
>>>>> to
>>>>> proceed.
>>>>> What would be nice is a way to get the project directory in the
>>>>> scripts,
>>>>> rather than their working directory.
>>>>> Does that make sense?
>>>>>
>>>>> Thank you in advance
>>>>> Best,
>>>>> Ivan
>>> ______________________________________________
>>> 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.
>
>______________________________________________
>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.