[R] project path in Rmd

[Ivan Calandra]

Thanks Jeff,

I was just completely unaware of these options! Now I know.

Best,
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 15:40, Jeff Newmiller wrote:
> 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
>>>> ______________________________________________
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>>>> 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.